21-46003541-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6
The NM_001848.3(COL6A1):c.2615G>A(p.Arg872Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,612,054 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R872W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001848.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A1 | NM_001848.3 | c.2615G>A | p.Arg872Gln | missense_variant | 35/35 | ENST00000361866.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A1 | ENST00000361866.8 | c.2615G>A | p.Arg872Gln | missense_variant | 35/35 | 1 | NM_001848.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152246Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000575 AC: 14AN: 243598Hom.: 0 AF XY: 0.0000450 AC XY: 6AN XY: 133264
GnomAD4 exome AF: 0.0000370 AC: 54AN: 1459690Hom.: 0 Cov.: 81 AF XY: 0.0000399 AC XY: 29AN XY: 726134
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152364Hom.: 0 Cov.: 35 AF XY: 0.000107 AC XY: 8AN XY: 74506
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Nov 11, 2021 | - - |
Bethlem myopathy 1A Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at