rs764600940
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 1P and 3B. PP2BP4BP6_Moderate
The NM_004370.6(COL12A1):c.5767G>A(p.Gly1923Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000828 in 1,448,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1923A) has been classified as Uncertain significance.
Frequency
Consequence
NM_004370.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL12A1 | NM_004370.6 | c.5767G>A | p.Gly1923Arg | missense_variant | 34/66 | ENST00000322507.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL12A1 | ENST00000322507.13 | c.5767G>A | p.Gly1923Arg | missense_variant | 34/66 | 1 | NM_004370.6 | P4 | |
COL12A1 | ENST00000345356.10 | c.2275G>A | p.Gly759Arg | missense_variant | 19/51 | 1 | |||
COL12A1 | ENST00000483888.6 | c.5767G>A | p.Gly1923Arg | missense_variant | 34/65 | 5 | A1 | ||
COL12A1 | ENST00000416123.6 | c.5767G>A | p.Gly1923Arg | missense_variant | 33/63 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000206 AC: 5AN: 242888Hom.: 0 AF XY: 0.00000759 AC XY: 1AN XY: 131730
GnomAD4 exome AF: 0.00000828 AC: 12AN: 1448884Hom.: 0 Cov.: 31 AF XY: 0.00000833 AC XY: 6AN XY: 719970
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at