rs145447965
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_004369.4(COL6A3):c.5341A>G(p.Ile1781Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000167 in 1,614,128 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. I1781I) has been classified as Likely benign.
Frequency
Consequence
NM_004369.4 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 |
---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.5341A>G | p.Ile1781Val | missense_variant | 11/44 | ENST00000295550.9 | |
COL6A3 | NM_057167.4 | c.4723A>G | p.Ile1575Val | missense_variant | 10/43 | ||
COL6A3 | NM_057166.5 | c.3520A>G | p.Ile1174Val | missense_variant | 8/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A3 | ENST00000295550.9 | c.5341A>G | p.Ile1781Val | missense_variant | 11/44 | 1 | NM_004369.4 | P1 | |
COL6A3 | ENST00000472056.5 | c.3520A>G | p.Ile1174Val | missense_variant | 8/41 | 1 | |||
COL6A3 | ENST00000353578.9 | c.4723A>G | p.Ile1575Val | missense_variant | 10/43 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000954 AC: 24AN: 251490Hom.: 0 AF XY: 0.0000956 AC XY: 13AN XY: 135918
GnomAD4 exome AF: 0.000176 AC: 258AN: 1461892Hom.: 0 Cov.: 32 AF XY: 0.000171 AC XY: 124AN XY: 727246
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74370
ClinVar
Submissions by phenotype
Ullrich congenital muscular dystrophy 1A;C4225336:Dystonia 27;CN029274:Bethlem myopathy 1A Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 03, 2015 | - - |
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at