Name: rs77928255
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.

rs77928255

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:99306663-99306664 (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: delCT
Variation Type: Deletion
Frequency: delCT=0.107613 (28484/264690, TOPMED)
delCT=0.097011 (13587/140056, GnomAD)
delCT=0.13099 (10308/78696, PAGE_STUDY) (+ 11 more)
delCT=0.07474 (2112/28258, 14KJPN)
delCT=0.08418 (1559/18520, ALFA)
delCT=0.07142 (1197/16760, 8.3KJPN)
delCT=0.1143 (732/6404, 1000G_30x)
delCT=0.1090 (546/5008, 1000G)
delCT=0.0859 (331/3854, ALSPAC)
delCT=0.0885 (328/3708, TWINSUK)
delCT=0.088 (88/998, GoNL)
delCT=0.110 (66/600, NorthernSweden)
delCT=0.037 (8/214, Vietnamese)
delCT=0.12 (5/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ADH1B : 3 Prime UTR 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18520	CT=0.91582	=0.08418
European	Sub	14152	CT=0.92496	=0.07504
African	Sub	2898	CT=0.9279	=0.0721
African Others	Sub	114	CT=0.930	=0.070
African American	Sub	2784	CT=0.9278	=0.0722
Asian	Sub	112	CT=0.964	=0.036
East Asian	Sub	86	CT=0.97	=0.03
Other Asian	Sub	26	CT=0.96	=0.04
Latin American 1	Sub	146	CT=0.884	=0.116
Latin American 2	Sub	610	CT=0.680	=0.320
South Asian	Sub	98	CT=0.97	=0.03
Other	Sub	504	CT=0.863	=0.137

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	CT=0.892387	delCT=0.107613
gnomAD - Genomes	Global	Study-wide	140056	CT=0.902989	delCT=0.097011
gnomAD - Genomes	European	Sub	75848	CT=0.91153	delCT=0.08847
gnomAD - Genomes	African	Sub	41976	CT=0.93087	delCT=0.06913
gnomAD - Genomes	American	Sub	13632	CT=0.76408	delCT=0.23592
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	CT=0.9142	delCT=0.0858
gnomAD - Genomes	East Asian	Sub	3130	CT=0.9240	delCT=0.0760
gnomAD - Genomes	Other	Sub	2148	CT=0.8901	delCT=0.1099
The PAGE Study	Global	Study-wide	78696	CT=0.86901	delCT=0.13099
The PAGE Study	AfricanAmerican	Sub	32512	CT=0.92956	delCT=0.07044
The PAGE Study	Mexican	Sub	10808	CT=0.68930	delCT=0.31070
The PAGE Study	Asian	Sub	8318	CT=0.9292	delCT=0.0708
The PAGE Study	PuertoRican	Sub	7918	CT=0.8440	delCT=0.1560
The PAGE Study	NativeHawaiian	Sub	4534	CT=0.9341	delCT=0.0659
The PAGE Study	Cuban	Sub	4230	CT=0.8962	delCT=0.1038
The PAGE Study	Dominican	Sub	3828	CT=0.9026	delCT=0.0974
The PAGE Study	CentralAmerican	Sub	2450	CT=0.6816	delCT=0.3184
The PAGE Study	SouthAmerican	Sub	1982	CT=0.6393	delCT=0.3607
The PAGE Study	NativeAmerican	Sub	1260	CT=0.8540	delCT=0.1460
The PAGE Study	SouthAsian	Sub	856	CT=0.946	delCT=0.054
14KJPN	JAPANESE	Study-wide	28258	CT=0.92526	delCT=0.07474
Allele Frequency Aggregator	Total	Global	18520	CT=0.91582	delCT=0.08418
Allele Frequency Aggregator	European	Sub	14152	CT=0.92496	delCT=0.07504
Allele Frequency Aggregator	African	Sub	2898	CT=0.9279	delCT=0.0721
Allele Frequency Aggregator	Latin American 2	Sub	610	CT=0.680	delCT=0.320
Allele Frequency Aggregator	Other	Sub	504	CT=0.863	delCT=0.137
Allele Frequency Aggregator	Latin American 1	Sub	146	CT=0.884	delCT=0.116
Allele Frequency Aggregator	Asian	Sub	112	CT=0.964	delCT=0.036
Allele Frequency Aggregator	South Asian	Sub	98	CT=0.97	delCT=0.03
8.3KJPN	JAPANESE	Study-wide	16760	CT=0.92858	delCT=0.07142
1000Genomes_30x	Global	Study-wide	6404	CT=0.8857	delCT=0.1143
1000Genomes_30x	African	Sub	1786	CT=0.9306	delCT=0.0694
1000Genomes_30x	Europe	Sub	1266	CT=0.9052	delCT=0.0948
1000Genomes_30x	South Asian	Sub	1202	CT=0.9626	delCT=0.0374
1000Genomes_30x	East Asian	Sub	1170	CT=0.9068	delCT=0.0932
1000Genomes_30x	American	Sub	980	CT=0.659	delCT=0.341
1000Genomes	Global	Study-wide	5008	CT=0.8910	delCT=0.1090
1000Genomes	African	Sub	1322	CT=0.9274	delCT=0.0726
1000Genomes	East Asian	Sub	1008	CT=0.9117	delCT=0.0883
1000Genomes	Europe	Sub	1006	CT=0.9066	delCT=0.0934
1000Genomes	South Asian	Sub	978	CT=0.962	delCT=0.038
1000Genomes	American	Sub	694	CT=0.669	delCT=0.331
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	CT=0.9141	delCT=0.0859
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	CT=0.9115	delCT=0.0885
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	CT=0.912	delCT=0.088
Northern Sweden	ACPOP	Study-wide	600	CT=0.890	delCT=0.110
A Vietnamese Genetic Variation Database	Global	Study-wide	214	CT=0.963	delCT=0.037
The Danish reference pan genome	Danish	Study-wide	40	CT=0.88	delCT=0.12

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 4	NC_000004.12:g.99306663_99306664del
GRCh37.p13 chr 4	NC_000004.11:g.100227820_100227821del
ADH1B RefSeqGene	NG_011435.1:g.19752_19753del

Gene: ADH1B, alcohol dehydrogenase 1B (class I), beta polypeptide (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ADH1B transcript variant 1	NM_000668.6:c.1176_1177=	N/A	3 Prime UTR Variant
ADH1B transcript variant 2	NM_001286650.2:c.1176_1… NM_001286650.2:c.1176_1177=	N/A	3 Prime UTR 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.

Not Reported in ClinVar

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	CT=	delCT
GRCh38.p14 chr 4	NC_000004.12:g.99306663_99306664=	NC_000004.12:g.99306663_99306664del
GRCh37.p13 chr 4	NC_000004.11:g.100227820_100227821=	NC_000004.11:g.100227820_100227821del
ADH1B RefSeqGene	NG_011435.1:g.19752_19753=	NG_011435.1:g.19752_19753del
ADH1B transcript variant 1	NM_000668.6:c.1176_1177=	NM_000668.6:c.1176_1177del
ADH1B transcript variant 1	NM_000668.5:c.1176_1177=	NM_000668.5:c.1176_1177del
ADH1B transcript	NM_000668.4:c.1176_1177=	NM_000668.4:c.1176_1177del
ADH1B transcript variant 2	NM_001286650.2:c.1176_1177=	NM_001286650.2:c.1176_1177del
ADH1B transcript variant 2	NM_001286650.1:c.1176_1177=	NM_001286650.1:c.1176_1177del

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#.

59 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	YUSUKE	ss5026818	Mar 15, 2016 (147)
2	RIKENSNPRC	ss5600846	Mar 15, 2016 (147)
3	EGP_SNPS	ss38318537	Mar 15, 2016 (147)
4	CGM_KYOTO	ss76859980	Mar 15, 2016 (147)
5	ILLUMINA	ss107695074	Mar 15, 2016 (147)
6	ILLUMINA	ss160649330	Dec 01, 2009 (131)
7	ILLUMINA	ss173658712	Mar 15, 2016 (147)
8	GMI	ss288561727	May 04, 2012 (138)
9	1000GENOMES	ss326552500	May 09, 2011 (138)
10	1000GENOMES	ss326585267	May 09, 2011 (138)
11	1000GENOMES	ss326760313	May 09, 2011 (138)
12	ILLUMINA	ss481811970	Dec 20, 2016 (150)
13	1000GENOMES	ss498802449	May 04, 2012 (138)
14	ILLUMINA	ss537202113	Dec 20, 2016 (150)
15	LUNTER	ss551393947	Apr 25, 2013 (138)
16	LUNTER	ss551521263	Apr 25, 2013 (138)
17	LUNTER	ss553150295	Apr 25, 2013 (138)
18	TISHKOFF	ss554110943	Apr 25, 2013 (138)
19	SSMP	ss663439692	Apr 01, 2015 (144)
20	EVA-GONL	ss980450587	Aug 21, 2014 (142)
21	1000GENOMES	ss1372537952	Aug 21, 2014 (142)
22	EVA_GENOME_DK	ss1576296060	Apr 01, 2015 (144)
23	EVA_DECODE	ss1589954664	Apr 01, 2015 (144)
24	EVA_UK10K_ALSPAC	ss1704278141	Apr 01, 2015 (144)
25	EVA_UK10K_TWINSUK	ss1704278743	Apr 01, 2015 (144)
26	HAMMER_LAB	ss1801910090	Sep 08, 2015 (146)
27	ILLUMINA	ss1946123020	Dec 20, 2016 (150)
28	ILLUMINA	ss1958706876	Feb 12, 2016 (147)
29	JJLAB	ss2030617818	Sep 14, 2016 (149)
30	ILLUMINA	ss2634154560	Nov 08, 2017 (151)
31	GNOMAD	ss2812859379	Nov 08, 2017 (151)
32	ILLUMINA	ss3022398544	Nov 08, 2017 (151)
33	MCHAISSO	ss3064982106	Nov 08, 2017 (151)
34	ILLUMINA	ss3625850219	Oct 12, 2018 (152)
35	ILLUMINA	ss3629025581	Oct 12, 2018 (152)
36	ILLUMINA	ss3636667759	Oct 12, 2018 (152)
37	ILLUMINA	ss3638501753	Oct 12, 2018 (152)
38	ILLUMINA	ss3643451929	Oct 12, 2018 (152)
39	ILLUMINA	ss3644855820	Oct 12, 2018 (152)
40	ILLUMINA	ss3652884782	Oct 12, 2018 (152)
41	EVA_DECODE	ss3712657705	Jul 13, 2019 (153)
42	ILLUMINA	ss3726155660	Jul 13, 2019 (153)
43	ACPOP	ss3731422196	Jul 13, 2019 (153)
44	ILLUMINA	ss3744238629	Jul 13, 2019 (153)
45	PAGE_CC	ss3771142571	Jul 13, 2019 (153)
46	KHV_HUMAN_GENOMES	ss3805315912	Jul 13, 2019 (153)
47	EVA	ss3828703779	Apr 26, 2020 (154)
48	TOPMED	ss4624655681	Apr 26, 2021 (155)
49	TOMMO_GENOMICS	ss5167080168	Apr 26, 2021 (155)
50	1000G_HIGH_COVERAGE	ss5260289869	Oct 13, 2022 (156)
51	HUGCELL_USP	ss5458932216	Oct 13, 2022 (156)
52	1000G_HIGH_COVERAGE	ss5541958514	Oct 13, 2022 (156)
53	SANFORD_IMAGENETICS	ss5635666409	Oct 13, 2022 (156)
54	TOMMO_GENOMICS	ss5701811959	Oct 13, 2022 (156)
55	YY_MCH	ss5805354280	Oct 13, 2022 (156)
56	EVA	ss5844424841	Oct 13, 2022 (156)
57	EVA	ss5854356157	Oct 13, 2022 (156)
58	EVA	ss5864678712	Oct 13, 2022 (156)
59	EVA	ss5964057175	Oct 13, 2022 (156)
60	1000Genomes	NC_000004.11 - 100227820	Oct 12, 2018 (152)
61	1000Genomes_30x	NC_000004.12 - 99306663	Oct 13, 2022 (156)
62	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 100227820	Oct 12, 2018 (152)
63	The Danish reference pan genome	NC_000004.11 - 100227820	Apr 26, 2020 (154)
64	gnomAD - Genomes	NC_000004.12 - 99306663	Apr 26, 2021 (155)
65	Genome of the Netherlands Release 5	NC_000004.11 - 100227820	Apr 26, 2020 (154)
66	Northern Sweden	NC_000004.11 - 100227820	Jul 13, 2019 (153)
67	The PAGE Study	NC_000004.12 - 99306663	Jul 13, 2019 (153)
68	8.3KJPN	NC_000004.11 - 100227820	Apr 26, 2021 (155)
69	14KJPN	NC_000004.12 - 99306663	Oct 13, 2022 (156)
70	TopMed	NC_000004.12 - 99306663	Apr 26, 2021 (155)
71	UK 10K study - Twins	NC_000004.11 - 100227820	Oct 12, 2018 (152)
72	A Vietnamese Genetic Variation Database	NC_000004.11 - 100227820	Jul 13, 2019 (153)
73	ALFA	NC_000004.12 - 99306663	Apr 26, 2021 (155)

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).

Associated ID	History Updated (Build)
rs4147540	Feb 20, 2003 (111)
rs146691255	Apr 25, 2013 (138)
rs386587427	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss160649330, ss288561727, ss326552500, ss326585267, ss326760313, ss551393947, ss551521263, ss553150295, ss1589954664, ss3643451929	NC_000004.10:100446842:CT:	NC_000004.12:99306662:CT:	(self)
22423682, 12473525, 930190, 5514061, 4707061, 25049475, 12473525, 2744515, ss481811970, ss498802449, ss537202113, ss554110943, ss663439692, ss980450587, ss1372537952, ss1576296060, ss1704278141, ss1704278743, ss1801910090, ss1946123020, ss1958706876, ss2030617818, ss2634154560, ss2812859379, ss3022398544, ss3625850219, ss3629025581, ss3636667759, ss3638501753, ss3644855820, ss3652884782, ss3731422196, ss3744238629, ss3828703779, ss5167080168, ss5635666409, ss5844424841, ss5964057175	NC_000004.11:100227819:CT:	NC_000004.12:99306662:CT:	(self)
29484449, 158846377, 364040, 35649063, 462033237, 4148172800, ss3064982106, ss3712657705, ss3726155660, ss3771142571, ss3805315912, ss4624655681, ss5260289869, ss5458932216, ss5541958514, ss5701811959, ss5805354280, ss5854356157, ss5864678712	NC_000004.12:99306662:CT:	NC_000004.12:99306662:CT:	(self)
ss5026818, ss5600846, ss38318537, ss76859980, ss107695074, ss173658712	NT_016354.19:24775540:CT:	NC_000004.12:99306662:CT:	(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 rs77928255

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

rs77928255