chr2-237363347-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004369.4(COL6A3):āc.5969G>Cā(p.Arg1990Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,614,000 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1990Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_004369.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.5969G>C | p.Arg1990Pro | missense_variant | 14/44 | ENST00000295550.9 | |
COL6A3 | NM_057167.4 | c.5351G>C | p.Arg1784Pro | missense_variant | 13/43 | ||
COL6A3 | NM_057166.5 | c.4148G>C | p.Arg1383Pro | missense_variant | 11/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A3 | ENST00000295550.9 | c.5969G>C | p.Arg1990Pro | missense_variant | 14/44 | 1 | NM_004369.4 | P1 | |
COL6A3 | ENST00000472056.5 | c.4148G>C | p.Arg1383Pro | missense_variant | 11/41 | 1 | |||
COL6A3 | ENST00000353578.9 | c.5351G>C | p.Arg1784Pro | missense_variant | 13/43 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152128Hom.: 0 Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461872Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727238
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152128Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74300
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at