rs777671647
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001848.3(COL6A1):āc.2899A>Gā(p.Ile967Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000237 in 1,604,694 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. I967I) has been classified as Likely benign.
Frequency
Consequence
NM_001848.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A1 | NM_001848.3 | c.2899A>G | p.Ile967Val | missense_variant | 35/35 | ENST00000361866.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A1 | ENST00000361866.8 | c.2899A>G | p.Ile967Val | missense_variant | 35/35 | 1 | NM_001848.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 152220Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 246612Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134182
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1452474Hom.: 0 Cov.: 34 AF XY: 0.00000694 AC XY: 5AN XY: 720740
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152220Hom.: 0 Cov.: 35 AF XY: 0.000161 AC XY: 12AN XY: 74360
ClinVar
Submissions by phenotype
not provided Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Oct 12, 2020 | Reported previously as a variant of uncertain significance in an individual with suspected diagnosis of linb-girdle muscular dystrophy (LGMD) (Nallamilli et al., 2018); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 30564623) - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | May 11, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 06, 2017 | - - |
Bethlem myopathy 1A Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 23, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at