rs770194625
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP2BP6
The NM_004370.6(COL12A1):c.5615G>A(p.Arg1872His) variant causes a missense change. The variant allele was found at a frequency of 0.000113 in 1,613,902 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R1872C) has been classified as Likely benign.
Frequency
Consequence
NM_004370.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL12A1 | NM_004370.6 | c.5615G>A | p.Arg1872His | missense_variant | 33/66 | ENST00000322507.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL12A1 | ENST00000322507.13 | c.5615G>A | p.Arg1872His | missense_variant | 33/66 | 1 | NM_004370.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000160 AC: 40AN: 249330Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135266
GnomAD4 exome AF: 0.000120 AC: 175AN: 1461828Hom.: 0 Cov.: 31 AF XY: 0.000125 AC XY: 91AN XY: 727222
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74272
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Feb 10, 2022 | Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant does not alter protein structure/function - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Feb 04, 2021 | - - |
Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at