rs41269303
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS1
The NM_004370.6(COL12A1):c.6641A>G(p.Gln2214Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000149 in 1,613,036 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. Q2214E) 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 -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL12A1 | NM_004370.6 | c.6641A>G | p.Gln2214Arg | missense_variant | 41/66 | ENST00000322507.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL12A1 | ENST00000322507.13 | c.6641A>G | p.Gln2214Arg | missense_variant | 41/66 | 1 | NM_004370.6 | P4 | |
COL12A1 | ENST00000345356.10 | c.3149A>G | p.Gln1050Arg | missense_variant | 26/51 | 1 | |||
COL12A1 | ENST00000483888.6 | c.6641A>G | p.Gln2214Arg | missense_variant | 41/65 | 5 | A1 | ||
COL12A1 | ENST00000416123.6 | c.6641A>G | p.Gln2214Arg | missense_variant | 40/63 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000868 AC: 132AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000198 AC: 49AN: 247718Hom.: 0 AF XY: 0.000119 AC XY: 16AN XY: 134402
GnomAD4 exome AF: 0.0000746 AC: 109AN: 1460808Hom.: 0 Cov.: 31 AF XY: 0.0000606 AC XY: 44AN XY: 726630
GnomAD4 genome ? AF: 0.000867 AC: 132AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.000739 AC XY: 55AN XY: 74436
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 14, 2020 | - - |
Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 30, 2023 | - - |
COL12A1-related condition Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 06, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at