rs375640580
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4BP6
The ENST00000295550.9(COL6A3):c.7192G>A(p.Val2398Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,612,502 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V2398L) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000295550.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.7192G>A | p.Val2398Ile | missense_variant | 36/44 | ENST00000295550.9 | NP_004360.2 | |
COL6A3 | NM_057167.4 | c.6574G>A | p.Val2192Ile | missense_variant | 35/43 | NP_476508.2 | ||
COL6A3 | NM_057166.5 | c.5371G>A | p.Val1791Ile | missense_variant | 33/41 | NP_476507.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL6A3 | ENST00000295550.9 | c.7192G>A | p.Val2398Ile | missense_variant | 36/44 | 1 | NM_004369.4 | ENSP00000295550 | P1 | |
COL6A3 | ENST00000472056.5 | c.5371G>A | p.Val1791Ile | missense_variant | 33/41 | 1 | ENSP00000418285 | |||
COL6A3 | ENST00000353578.9 | c.6574G>A | p.Val2192Ile | missense_variant | 35/43 | 5 | ENSP00000315873 | |||
COL6A3 | ENST00000491769.1 | n.1446G>A | non_coding_transcript_exon_variant | 13/20 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000362 AC: 9AN: 248564Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134826
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1460348Hom.: 0 Cov.: 34 AF XY: 0.0000262 AC XY: 19AN XY: 726530
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Aug 14, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Apr 28, 2021 | Previously reported as a variant of uncertain significance in an individual with a clinical diagnosis of LGMD; variants in other genes that may influence the phenotype were also obsevered (Fichna et al., 2018); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 29970176) - |
COL6A3-related disorder Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 15, 2024 | The COL6A3 c.7192G>A variant is predicted to result in the amino acid substitution p.Val2398Ile. This variant has been previously reported in the compound heterozygous state in an individual with limb-girdle muscular dystrophy (Table 1, Fichna et al. 2018. PubMed ID: 29970176). This variant is reported in 0.026% of alleles in individuals of African descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Bethlem myopathy 1A Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at