rs140517685
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_001848.3(COL6A1):c.1681G>A(p.Asp561Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000662 in 1,600,250 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). Synonymous variant affecting the same amino acid position (i.e. D561D) has been classified as Likely benign.
Frequency
Consequence
NM_001848.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A1 | NM_001848.3 | c.1681G>A | p.Asp561Asn | missense_variant | 26/35 | ENST00000361866.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A1 | ENST00000361866.8 | c.1681G>A | p.Asp561Asn | missense_variant | 26/35 | 1 | NM_001848.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152264Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000659 AC: 15AN: 227762Hom.: 0 AF XY: 0.0000814 AC XY: 10AN XY: 122794
GnomAD4 exome AF: 0.0000698 AC: 101AN: 1447868Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 58AN XY: 718740
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152382Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74508
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Apr 01, 2019 | - - |
Bethlem myopathy 1A Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at