Name: rs147297176
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs147297176

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:26090938 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000189 (50/264690, TOPMED)
T=0.000060 (15/251488, GnomAD_exome)
T=0.000186 (26/140140, GnomAD) (+ 9 more)
T=0.000074 (9/121412, ExAC)
T=0.00008 (3/35432, ALFA)
T=0.00011 (3/28258, 14KJPN)
T=0.00006 (1/16760, 8.3KJPN)
T=0.00031 (4/13006, GO-ESP)
T=0.0002 (1/6404, 1000G_30x)
T=0.0002 (1/5008, 1000G)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)

Clinical Significance: Reported in ClinVar
Gene : Consequence: HFE : Synonymous Variant
HFE-AS1 : Non Coding Transcript Variant
Publications: 0 citations
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	51794	C=0.99988	T=0.00012
European	Sub	36678	C=1.00000	T=0.00000
African	Sub	7756	C=0.9994	T=0.0006
African Others	Sub	298	C=1.000	T=0.000
African American	Sub	7458	C=0.9993	T=0.0007
Asian	Sub	112	C=1.000	T=0.000
East Asian	Sub	86	C=1.00	T=0.00
Other Asian	Sub	26	C=1.00	T=0.00
Latin American 1	Sub	500	C=1.000	T=0.000
Latin American 2	Sub	628	C=1.000	T=0.000
South Asian	Sub	98	C=1.00	T=0.00
Other	Sub	6022	C=0.9998	T=0.0002

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.999811	T=0.000189
gnomAD - Exomes	Global	Study-wide	251488	C=0.999940	T=0.000060
gnomAD - Exomes	European	Sub	135412	C=0.999985	T=0.000015
gnomAD - Exomes	Asian	Sub	49010	C=0.99996	T=0.00004
gnomAD - Exomes	American	Sub	34592	C=0.99997	T=0.00003
gnomAD - Exomes	African	Sub	16256	C=0.99938	T=0.00062
gnomAD - Exomes	Ashkenazi Jewish	Sub	10080	C=1.00000	T=0.00000
gnomAD - Exomes	Other	Sub	6138	C=1.0000	T=0.0000
gnomAD - Genomes	Global	Study-wide	140140	C=0.999814	T=0.000186
gnomAD - Genomes	European	Sub	75898	C=1.00000	T=0.00000
gnomAD - Genomes	African	Sub	41992	C=0.99940	T=0.00060
gnomAD - Genomes	American	Sub	13644	C=0.99993	T=0.00007
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=1.0000	T=0.0000
gnomAD - Genomes	East Asian	Sub	3130	C=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2152	C=1.0000	T=0.0000
ExAC	Global	Study-wide	121412	C=0.999926	T=0.000074
ExAC	Europe	Sub	73354	C=0.99999	T=0.00001
ExAC	Asian	Sub	25166	C=0.99996	T=0.00004
ExAC	American	Sub	11578	C=0.99991	T=0.00009
ExAC	African	Sub	10406	C=0.99942	T=0.00058
ExAC	Other	Sub	908	C=1.000	T=0.000
Allele Frequency Aggregator	Total	Global	35432	C=0.99992	T=0.00008
Allele Frequency Aggregator	European	Sub	26588	C=1.00000	T=0.00000
Allele Frequency Aggregator	Other	Sub	4588	C=0.9998	T=0.0002
Allele Frequency Aggregator	African	Sub	2918	C=0.9993	T=0.0007
Allele Frequency Aggregator	Latin American 2	Sub	628	C=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	500	C=1.000	T=0.000
Allele Frequency Aggregator	Asian	Sub	112	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	T=0.00
14KJPN	JAPANESE	Study-wide	28258	C=0.99989	T=0.00011
8.3KJPN	JAPANESE	Study-wide	16760	C=0.99994	T=0.00006
GO Exome Sequencing Project	Global	Study-wide	13006	C=0.99969	T=0.00031
GO Exome Sequencing Project	European American	Sub	8600	C=1.0000	T=0.0000
GO Exome Sequencing Project	African American	Sub	4406	C=0.9991	T=0.0009
1000Genomes_30x	Global	Study-wide	6404	C=0.9998	T=0.0002
1000Genomes_30x	African	Sub	1786	C=1.0000	T=0.0000
1000Genomes_30x	Europe	Sub	1266	C=1.0000	T=0.0000
1000Genomes_30x	South Asian	Sub	1202	C=1.0000	T=0.0000
1000Genomes_30x	East Asian	Sub	1170	C=0.9991	T=0.0009
1000Genomes_30x	American	Sub	980	C=1.000	T=0.000
1000Genomes	Global	Study-wide	5008	C=0.9998	T=0.0002
1000Genomes	African	Sub	1322	C=1.0000	T=0.0000
1000Genomes	East Asian	Sub	1008	C=0.9990	T=0.0010
1000Genomes	Europe	Sub	1006	C=1.0000	T=0.0000
1000Genomes	South Asian	Sub	978	C=1.000	T=0.000
1000Genomes	American	Sub	694	C=1.000	T=0.000
SGDP_PRJ	Global	Study-wide	2	C=0.5	T=0.5

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 6	NC_000006.12:g.26090938C>T
GRCh37.p13 chr 6	NC_000006.11:g.26091166C>T
HFE RefSeqGene (LRG_748)	NG_008720.2:g.8658C>T

Gene: HFE, homeostatic iron regulator (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
HFE transcript variant 7	NM_139007.3:c.77-376C>T	N/A	Intron Variant
HFE transcript variant 8	NM_139008.3:c.77-376C>T	N/A	Intron Variant
HFE transcript variant 10	NM_139010.3:c.77-1747C>T	N/A	Intron Variant
HFE transcript variant 11	NM_139011.3:c.77-2181C>T	N/A	Intron Variant
HFE transcript variant 4	NM_139004.3:c.174C>T	F [TTC] > F [TTT]	Coding Sequence Variant
hereditary hemochromatosis protein isoform 4 precursor	NP_620573.1:p.Phe58=	F (Phe) > F (Phe)	Synonymous Variant
HFE transcript variant 3	NM_139003.3:c.174C>T	F [TTC] > F [TTT]	Coding Sequence Variant
hereditary hemochromatosis protein isoform 3 precursor	NP_620572.1:p.Phe58=	F (Phe) > F (Phe)	Synonymous Variant
HFE transcript variant 12	NM_001300749.2:c.174C>T	F [TTC] > F [TTT]	Coding Sequence Variant
hereditary hemochromatosis protein isoform 12 precursor	NP_001287678.1:p.Phe58=	F (Phe) > F (Phe)	Synonymous Variant
HFE transcript variant 6	NM_139006.3:c.174C>T	F [TTC] > F [TTT]	Coding Sequence Variant
hereditary hemochromatosis protein isoform 6 precursor	NP_620575.1:p.Phe58=	F (Phe) > F (Phe)	Synonymous Variant
HFE transcript variant 9	NM_139009.3:c.105C>T	F [TTC] > F [TTT]	Coding Sequence Variant
hereditary hemochromatosis protein isoform 9 precursor	NP_620578.1:p.Phe35=	F (Phe) > F (Phe)	Synonymous Variant
HFE transcript variant 13	NM_001384164.1:c.174C>T	F [TTC] > F [TTT]	Coding Sequence Variant
hereditary hemochromatosis protein isoform 13 precursor	NP_001371093.1:p.Phe58=	F (Phe) > F (Phe)	Synonymous Variant
HFE transcript variant 1	NM_000410.4:c.174C>T	F [TTC] > F [TTT]	Coding Sequence Variant
hereditary hemochromatosis protein isoform 1 precursor	NP_000401.1:p.Phe58=	F (Phe) > F (Phe)	Synonymous Variant
HFE transcript variant X1	XR_241893.5:n.186C>T	N/A	Non Coding Transcript Variant

Gene: HFE-AS1, HFE antisense RNA 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
HFE-AS1 transcript	NR_144383.1:n.97G>A	N/A	Non Coding Transcript Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: T (allele ID: 1137478 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001479459.5	Hereditary hemochromatosis	Likely-Benign

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	C=	T
GRCh38.p14 chr 6	NC_000006.12:g.26090938=	NC_000006.12:g.26090938C>T
GRCh37.p13 chr 6	NC_000006.11:g.26091166=	NC_000006.11:g.26091166C>T
HFE RefSeqGene (LRG_748)	NG_008720.2:g.8658=	NG_008720.2:g.8658C>T
HFE transcript variant 1	NM_000410.4:c.174=	NM_000410.4:c.174C>T
HFE transcript variant 1	NM_000410.3:c.174=	NM_000410.3:c.174C>T
HFE transcript variant 6	NM_139006.3:c.174=	NM_139006.3:c.174C>T
HFE transcript variant 6	NM_139006.2:c.174=	NM_139006.2:c.174C>T
HFE transcript variant 9	NM_139009.3:c.105=	NM_139009.3:c.105C>T
HFE transcript variant 9	NM_139009.2:c.105=	NM_139009.2:c.105C>T
HFE transcript variant 12	NM_001300749.3:c.174=	NM_001300749.3:c.174C>T
HFE transcript variant 12	NM_001300749.2:c.174=	NM_001300749.2:c.174C>T
HFE transcript variant 12	NM_001300749.1:c.174=	NM_001300749.1:c.174C>T
HFE transcript variant 4	NM_139004.3:c.174=	NM_139004.3:c.174C>T
HFE transcript variant 4	NM_139004.2:c.174=	NM_139004.2:c.174C>T
HFE transcript variant 3	NM_139003.3:c.174=	NM_139003.3:c.174C>T
HFE transcript variant 3	NM_139003.2:c.174=	NM_139003.2:c.174C>T
HFE transcript variant 14	NM_001406751.1:c.174=	NM_001406751.1:c.174C>T
HFE transcript variant 13	NM_001384164.1:c.174=	NM_001384164.1:c.174C>T
HFE transcript variant X1	XR_241893.5:n.186=	XR_241893.5:n.186C>T
HFE transcript variant X2	XR_241893.4:n.268=	XR_241893.4:n.268C>T
HFE transcript variant X2	XR_241893.3:n.296=	XR_241893.3:n.296C>T
HFE transcript variant X2	XR_241893.2:n.296=	XR_241893.2:n.296C>T
HFE transcript variant X2	XR_241893.1:n.296=	XR_241893.1:n.296C>T
HFE transcript variant 5	NM_139005.2:c.174=	NM_139005.2:c.174C>T
HFE transcript variant 2	NM_139002.2:c.174=	NM_139002.2:c.174C>T
HFE-AS1 transcript	NR_144383.1:n.97=	NR_144383.1:n.97G>A
HFE transcript variant 5	NM_139005.1:c.174=	NM_139005.1:c.174C>T
HFE transcript variant 2	NM_139002.1:c.174=	NM_139002.1:c.174C>T
hereditary hemochromatosis protein isoform 1 precursor	NP_000401.1:p.Phe58=	NP_000401.1:p.Phe58=
hereditary hemochromatosis protein isoform 6 precursor	NP_620575.1:p.Phe58=	NP_620575.1:p.Phe58=
hereditary hemochromatosis protein isoform 9 precursor	NP_620578.1:p.Phe35=	NP_620578.1:p.Phe35=
hereditary hemochromatosis protein isoform 12 precursor	NP_001287678.1:p.Phe58=	NP_001287678.1:p.Phe58=
hereditary hemochromatosis protein isoform 4 precursor	NP_620573.1:p.Phe58=	NP_620573.1:p.Phe58=
hereditary hemochromatosis protein isoform 3 precursor	NP_620572.1:p.Phe58=	NP_620572.1:p.Phe58=
hereditary hemochromatosis protein isoform 13 precursor	NP_001371093.1:p.Phe58=	NP_001371093.1:p.Phe58=
HFE transcript variant 7	NM_139007.2:c.77-376=	NM_139007.2:c.77-376C>T
HFE transcript variant 7	NM_139007.3:c.77-376=	NM_139007.3:c.77-376C>T
HFE transcript variant 8	NM_139008.2:c.77-376=	NM_139008.2:c.77-376C>T
HFE transcript variant 8	NM_139008.3:c.77-376=	NM_139008.3:c.77-376C>T
HFE transcript variant 10	NM_139010.2:c.77-1747=	NM_139010.2:c.77-1747C>T
HFE transcript variant 10	NM_139010.3:c.77-1747=	NM_139010.3:c.77-1747C>T
HFE transcript variant 11	NM_139011.2:c.77-2181=	NM_139011.2:c.77-2181C>T
HFE transcript variant 11	NM_139011.3:c.77-2181=	NM_139011.3:c.77-2181C>T

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

18 SubSNP, 11 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	NHLBI-ESP	ss342203115	May 09, 2011 (134)
2	1000GENOMES	ss488830354	May 04, 2012 (137)
3	1000GENOMES	ss1319404488	Aug 21, 2014 (142)
4	EVA_EXAC	ss1688187404	Apr 01, 2015 (144)
5	HUMAN_LONGEVITY	ss2282674226	Dec 20, 2016 (150)
6	GNOMAD	ss2735584180	Nov 08, 2017 (151)
7	GNOMAD	ss2747561165	Nov 08, 2017 (151)
8	GNOMAD	ss2836999870	Nov 08, 2017 (151)
9	EVA	ss3764754570	Jul 13, 2019 (153)
10	EVA	ss3824161834	Apr 26, 2020 (154)
11	SGDP_PRJ	ss3864147637	Apr 26, 2020 (154)
12	TOPMED	ss4697235567	Apr 26, 2021 (155)
13	TOMMO_GENOMICS	ss5176647013	Apr 26, 2021 (155)
14	EVA	ss5364498339	Oct 13, 2022 (156)
15	1000G_HIGH_COVERAGE	ss5553392385	Oct 13, 2022 (156)
16	TOMMO_GENOMICS	ss5714450921	Oct 13, 2022 (156)
17	YY_MCH	ss5807251621	Oct 13, 2022 (156)
18	EVA	ss5883096390	Oct 13, 2022 (156)
19	1000Genomes	NC_000006.11 - 26091166	Oct 12, 2018 (152)
20	1000Genomes_30x	NC_000006.12 - 26090938	Oct 13, 2022 (156)
21	ExAC	NC_000006.11 - 26091166	Oct 12, 2018 (152)
22	gnomAD - Genomes	NC_000006.12 - 26090938	Apr 26, 2021 (155)
23	gnomAD - Exomes	NC_000006.11 - 26091166	Jul 13, 2019 (153)
24	GO Exome Sequencing Project	NC_000006.11 - 26091166	Oct 12, 2018 (152)
25	SGDP_PRJ	NC_000006.11 - 26091166	Apr 26, 2020 (154)
26	8.3KJPN	NC_000006.11 - 26091166	Apr 26, 2021 (155)
27	14KJPN	NC_000006.12 - 26090938	Oct 13, 2022 (156)
28	TopMed	NC_000006.12 - 26090938	Apr 26, 2021 (155)
29	ALFA	NC_000006.12 - 26090938	Apr 26, 2021 (155)
30	ClinVar	RCV001479459.5	Oct 13, 2022 (156)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
31165437, 8208859, 4723243, 619876, 16164617, 34616320, ss342203115, ss488830354, ss1319404488, ss1688187404, ss2735584180, ss2747561165, ss2836999870, ss3764754570, ss3824161834, ss3864147637, ss5176647013, ss5364498339	NC_000006.11:26091165:C:T	NC_000006.12:26090937:C:T	(self)
RCV001479459.5, 40918320, 220179599, 48288025, 534613125, 1457262404, ss2282674226, ss4697235567, ss5553392385, ss5714450921, ss5807251621, ss5883096390	NC_000006.12:26090937:C:T	NC_000006.12:26090937:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs147297176

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs147297176