rs144223596
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The ENST00000295550.9(COL6A3):c.4510C>T(p.Arg1504Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000876 in 1,614,116 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. R1504R) has been classified as Likely benign.
Frequency
Consequence
ENST00000295550.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.4510C>T | p.Arg1504Trp | missense_variant | 10/44 | ENST00000295550.9 | NP_004360.2 | |
COL6A3 | NM_057167.4 | c.3892C>T | p.Arg1298Trp | missense_variant | 9/43 | NP_476508.2 | ||
COL6A3 | NM_057166.5 | c.2689C>T | p.Arg897Trp | missense_variant | 7/41 | NP_476507.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL6A3 | ENST00000295550.9 | c.4510C>T | p.Arg1504Trp | missense_variant | 10/44 | 1 | NM_004369.4 | ENSP00000295550 | P1 | |
COL6A3 | ENST00000472056.5 | c.2689C>T | p.Arg897Trp | missense_variant | 7/41 | 1 | ENSP00000418285 | |||
COL6A3 | ENST00000353578.9 | c.3892C>T | p.Arg1298Trp | missense_variant | 9/43 | 5 | ENSP00000315873 | |||
COL6A3 | ENST00000684597.1 | c.117-277C>T | intron_variant | ENSP00000508021 |
Frequencies
GnomAD3 genomes AF: 0.000618 AC: 94AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000434 AC: 109AN: 251426Hom.: 0 AF XY: 0.000434 AC XY: 59AN XY: 135894
GnomAD4 exome AF: 0.000903 AC: 1320AN: 1461894Hom.: 2 Cov.: 38 AF XY: 0.000844 AC XY: 614AN XY: 727248
GnomAD4 genome AF: 0.000618 AC: 94AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.000565 AC XY: 42AN XY: 74378
ClinVar
Submissions by phenotype
not provided Uncertain:5
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 15, 2018 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 03, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Mar 18, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2022 | Reported previously in the heterozygous state as a variant of uncertain significance in an individual with limb-girdle muscular dystrophy (Nallamilli et al., 2018); Reported along with a second COL6A3 variant in a patient with segmental and cervical dystonia and tremor; however, segregation information was not available (Kumar et al., 2019); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 29411265, 30564623, 31731261) - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 29, 2024 | Variant summary: COL6A3 c.4510C>T (p.Arg1504Trp) results in a non-conservative amino acid change located in the von Willebrand factor, type A domain (IPR002035) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00088 in 1614116 control chromosomes in the gnomAD database, including 2 homozygotes. c.4510C>T has been reported in the literature in individuals affected with clinical features of COL6A3-related conditions (e.g. Kumar_2019, Meinke_2020, Nallamilli_2018). These reports do not provide unequivocal conclusions about association of the variant with Ullrich Congenital Muscular Dystrophy 1. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 31731261, 31862442, 30564623). ClinVar contains an entry for this variant (Variation ID: 166943). Based on the evidence outlined above, the variant was classified as uncertain significance. - |
Collagen 6-related myopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at