NM_000492.4(CFTR):c.274-6T>C AND Cystic fibrosis

Germline classification:: Benign/Likely benign (6 submissions)
Last evaluated:: Jan 31, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000231663.29

Allele description [Variation Report for NM_000492.4(CFTR):c.274-6T>C]

NM_000492.4(CFTR):c.274-6T>C

Gene:

CFTR:CF transmembrane conductance regulator [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q31.2

Genomic location:

Preferred name:

NM_000492.4(CFTR):c.274-6T>C

HGVS:

NC_000007.14:g.117530893T>C
NG_016465.4:g.70110T>C
NM_000492.4:c.274-6T>CMANE SELECT
LRG_663t1:c.274-6T>C
LRG_663:g.70110T>C
NC_000007.13:g.117170947T>C
NM_000492.3:c.274-6T>C
NM_000492.4:c.274-6T>C

Links:

dbSNP: rs371315549

NCBI 1000 Genomes Browser:

rs371315549

Molecular consequence:

NM_000492.4:c.274-6T>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Cystic fibrosis (CF)
Synonyms:: Mucoviscidosis
Identifiers:: MONDO: MONDO:0009061; MedGen: C0010674; Orphanet: 586; OMIM: 219700

Recent activity

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PREDICTED: Homo sapiens DNA polymerase beta (POLB), transcript variant X3, mRNA
PREDICTED: Homo sapiens DNA polymerase beta (POLB), transcript variant X3, mRNA
gi|2217372328|ref|XM_005273537.5|

Nucleotide
MAG: Aeromicrobium sp. REDSEA-S42_B4 scaffold11, whole genome shotgun sequence
MAG: Aeromicrobium sp. REDSEA-S42_B4 scaffold11, whole genome shotgun sequence
gi|1021399061|gb|LUNI01000011.1||gn :LUNI01|scaffold11

Nucleotide
leaf, Zn_CMV_3
leaf, Zn_CMV_3

biosample
Cirrenalia macrocephala strain MUCL 15736 28S ribosomal RNA gene, partial sequen...
Cirrenalia macrocephala strain MUCL 15736 28S ribosomal RNA gene, partial sequence
gi|61676480|gb|AY856915.1|

Nucleotide
de96c11.x3 Wellcome CRC pRN3 St19 26 Xenopus laevis cDNA clone IMAGE:3549333 3' ...
de96c11.x3 Wellcome CRC pRN3 St19 26 Xenopus laevis cDNA clone IMAGE:3549333 3' similar to SW:VATX_BOVIN P12953 VACUOLAR ATP SYNTHASE SUBUNIT AC39, mRNA sequence
gi|13565985|gnl|dbEST|8294214|gb|BG 5.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000285000	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 31, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000886361	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2019)	Benign (Aug 22, 2023)	germline	clinical testing	Citation Link,
SCV001453946	Natera, Inc.	no assertion criteria provided	Likely benign (Aug 7, 2019)	germline	clinical testing
SCV001821988	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jul 22, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002749442	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Jan 22, 2019)	germline	clinical testing	Citation Link,
SCV003839064	Johns Hopkins Genomics, Johns Hopkins University	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Feb 14, 2023)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 10601093, 20717170, 21198395, 23381846, 25781545, 25741868

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Complete mutational screening of the cystic fibrosis transmembrane conductance regulator gene: cystic fibrosis mutations are not involved in healthy men with reduced sperm quality.

Pallares-Ruiz N, Carles S, Des Georges M, Guittard C, Arnal F, Humeau C, Claustres M.

Hum Reprod. 1999 Dec;14(12):3035-40.

PubMed [citation]

PMID:: 10601093

See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000285000.10

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mendelics, SCV000886361.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Natera, Inc., SCV001453946.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV001821988.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Ambry Genetics, SCV002749442.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Johns Hopkins Genomics, Johns Hopkins University, SCV003839064.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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