VCV000130009.38 - ClinVar

NM_001077365.2(POMT1):c.1826-6C>A

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(9)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Benign/Likely benign

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001077365.2(POMT1):c.1826-6C>A

Variation ID: 130009 Accession: VCV000130009.38

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 9q34.13 9: 131522041 (GRCh38) [ NCBI UCSC ] 9: 134397428 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	May 17, 2014	Oct 20, 2024	Aug 1, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_001077365.2:c.1826-6C>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		intron variant
NM_001077366.2:c.1664-6C>A		intron variant
NM_001136113.2:c.1826-6C>A		intron variant
NM_001136114.2:c.1475-6C>A		intron variant
NM_001353193.2:c.1892-6C>A		intron variant
NM_001353194.2:c.1664-6C>A		intron variant
NM_001353195.2:c.1475-6C>A		intron variant
NM_001353196.2:c.1736-6C>A		intron variant
NM_001353197.2:c.1730-6C>A		intron variant
NM_001353198.2:c.1730-6C>A		intron variant
NM_001353199.2:c.1541-6C>A		intron variant
NM_001353200.2:c.1370-6C>A		intron variant
NM_001374689.1:c.1814-6C>A		intron variant
NM_001374690.1:c.1607-6C>A		intron variant
NM_001374691.1:c.1475-6C>A		intron variant
NM_001374692.1:c.1475-6C>A		intron variant
NM_001374693.1:c.1475-6C>A		intron variant
NM_001374695.1:c.1436-6C>A		intron variant
NM_007171.4:c.1892-6C>A		intron variant
NC_000009.12:g.131522041C>A
NC_000009.11:g.134397428C>A
NG_008896.2:g.24140C>A
LRG_842:g.24140C>A
LRG_842t1:c.1892-6C>A
LRG_842t2:c.1826-6C>A

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000009.12:131522040:C:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

0.00280 (A)

Allele frequency Help The frequency of the allele represented by this VCV record.

1000 Genomes Project 0.00280

1000 Genomes Project 30x 0.00297

The Genome Aggregation Database (gnomAD), exomes 0.00696

Exome Aggregation Consortium (ExAC) 0.00699

Trans-Omics for Precision Medicine (TOPMed) 0.00773

The Genome Aggregation Database (gnomAD) 0.00816

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01061

Links

ClinGen: CA154751 dbSNP: rs140258585 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
POMT1		-	-	GRCh38 GRCh37	1161	1202

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not specified	Benign (4)	criteria provided, multiple submitters, no conflicts	Mar 15, 2016	RCV000118033.17
Autosomal recessive limb-girdle muscular dystrophy type 2K	Likely benign (1)	criteria provided, single submitter	Jan 13, 2018	RCV000292825.7
not provided	Benign/Likely benign (3)	criteria provided, multiple submitters, no conflicts	Aug 1, 2024	RCV000712819.25
Autosomal recessive limb-girdle muscular dystrophy type 2K Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1 Walker-Warburg congenital muscular dystrophy	Benign (1)	criteria provided, single submitter	Dec 31, 2019	RCV001086685.6

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	NOT SPECIFIED Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV000311746.1 First in ClinVar: Oct 02, 2016 Last updated: Oct 02, 2016
Benign (Mar 16, 2018)	criteria provided, single submitter (Athena Diagnostics Criteria) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Athena Diagnostics Accession: SCV000843353.1 First in ClinVar: Oct 20, 2018 Last updated: Oct 20, 2018
Benign (Jan 13, 2015)	criteria provided, single submitter (LMM Criteria) Method: clinical testing	not specified Affected status: not provided Allele origin: germline	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine Accession: SCV000711700.2 First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018	Comment: c.1892-6C>A in intron 18 of POMT1: This variant is not expected to have clinical significance because it has been identified in 1.5% (125/8600) of European … (more) c.1892-6C>A in intron 18 of POMT1: This variant is not expected to have clinical significance because it has been identified in 1.5% (125/8600) of European Amer ican chromosomes from a broad population by the NHLBI Exome Sequencing Project ( http://evs.gs.washington.edu/EVS; dbSNP rs140258585). (less) Number of individuals with the variant: 1
Benign (Dec 31, 2019)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B1 Walker-Warburg congenital muscular dystrophy Limb-girdle muscular dystrophy-dystroglycanopathy, type C1 Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001120766.2 First in ClinVar: Dec 17, 2019 Last updated: May 04, 2020
Likely benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: not provided	not provided (Autosomal recessive inheritance) Affected status: yes Allele origin: germline	Breakthrough Genomics, Breakthrough Genomics Accession: SCV005225936.1 First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024
Benign (Sep 30, 2013)	criteria provided, single submitter (ACMG Guidelines, 2007) Method: clinical testing	AllHighlyPenetrant (Autosomal recessive inheritance) Affected status: unknown Allele origin: germline	Genetic Services Laboratory, University of Chicago Accession: SCV000152354.1 First in ClinVar: May 17, 2014 Last updated: May 17, 2014
Benign (Mar 15, 2016)	criteria provided, single submitter (GeneDx Variant Classification (06012015)) Method: clinical testing	not specified Affected status: yes Allele origin: germline	GeneDx Accession: SCV000514253.4 First in ClinVar: Mar 08, 2017 Last updated: Apr 09, 2018	Comment: This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more) This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. (less)
Likely benign (Jan 13, 2018)	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019) Method: clinical testing	Autosomal recessive limb-girdle muscular dystrophy type 2K Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV000477673.3 First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020	Comment: This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more) This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. (less)
Benign (Aug 01, 2024)	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2) Method: clinical testing	not provided Affected status: yes Allele origin: germline	CeGaT Center for Human Genetics Tuebingen Accession: SCV002498060.18 First in ClinVar: Apr 08, 2022 Last updated: Oct 20, 2024	Comment: POMT1: BP4, BS1, BS2 Number of individuals with the variant: 18

Comment:

c.1892-6C>A in intron 18 of POMT1: This variant is not expected to have clinical significance because it has been identified in 1.5% (125/8600) of European Amer ican chromosomes from a broad population by the NHLBI Exome Sequencing Project ( http://evs.gs.washington.edu/EVS; dbSNP rs140258585).

Comment:

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

Comment:

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs140258585 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 20, 2024

ClinVar Genomic variation as it relates to human health

NM_001077365.2(POMT1):c.1826-6C>A

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs140258585 ...