rs371111712
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6
The NM_001848.3(COL6A1):c.2852C>T(p.Thr951Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,611,728 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T951T) 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 -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A1 | NM_001848.3 | c.2852C>T | p.Thr951Met | missense_variant | 35/35 | ENST00000361866.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A1 | ENST00000361866.8 | c.2852C>T | p.Thr951Met | missense_variant | 35/35 | 1 | NM_001848.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152252Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000526 AC: 13AN: 247036Hom.: 0 AF XY: 0.0000446 AC XY: 6AN XY: 134524
GnomAD4 exome AF: 0.000106 AC: 155AN: 1459476Hom.: 1 Cov.: 34 AF XY: 0.000117 AC XY: 85AN XY: 725848
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152252Hom.: 0 Cov.: 34 AF XY: 0.000108 AC XY: 8AN XY: 74394
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Aug 16, 2022 | Identified in trans with another variant in a patient with sporadic progressive bulbar palsy who also harbored a homozygous variant in the KIAA1755 gene; however, evidence in support of pathogenicity for the KIAA1755 variant was not provided in the report (Steinberg et al., 2015); 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: 25773295) - |
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at