6-75138453-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_004370.6(COL12A1):c.5225G>A(p.Arg1742His) variant causes a missense change. The variant allele was found at a frequency of 0.0036 in 1,613,066 control chromosomes in the GnomAD database, including 151 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1742C) has been classified as Uncertain significance.
Frequency
Consequence
NM_004370.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL12A1 | NM_004370.6 | c.5225G>A | p.Arg1742His | missense_variant | 29/66 | ENST00000322507.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL12A1 | ENST00000322507.13 | c.5225G>A | p.Arg1742His | missense_variant | 29/66 | 1 | NM_004370.6 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0187 AC: 2845AN: 152114Hom.: 85 Cov.: 32
GnomAD3 exomes AF: 0.00509 AC: 1263AN: 247950Hom.: 30 AF XY: 0.00387 AC XY: 521AN XY: 134468
GnomAD4 exome AF: 0.00203 AC: 2964AN: 1460834Hom.: 66 Cov.: 31 AF XY: 0.00176 AC XY: 1276AN XY: 726648
GnomAD4 genome AF: 0.0187 AC: 2848AN: 152232Hom.: 85 Cov.: 32 AF XY: 0.0182 AC XY: 1353AN XY: 74438
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at