chr6-75090220-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP2BS1_Supporting
The NM_004370.6(COL12A1):c.8831C>T(p.Pro2944Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000247 in 1,614,000 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. P2944A) 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.8831C>T | p.Pro2944Leu | missense_variant | 63/66 | ENST00000322507.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL12A1 | ENST00000322507.13 | c.8831C>T | p.Pro2944Leu | missense_variant | 63/66 | 1 | NM_004370.6 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000408 AC: 62AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000277 AC: 69AN: 249360Hom.: 0 AF XY: 0.000236 AC XY: 32AN XY: 135330
GnomAD4 exome AF: 0.000230 AC: 336AN: 1461770Hom.: 0 Cov.: 31 AF XY: 0.000223 AC XY: 162AN XY: 727194
GnomAD4 genome AF: 0.000407 AC: 62AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.000457 AC XY: 34AN XY: 74430
ClinVar
Submissions by phenotype
not provided Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | May 05, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2016 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Oct 03, 2023 | Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function - |
Bethlem myopathy 2 Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics Laboratory, University Hospital Schleswig-Holstein | Aug 31, 2021 | - - |
Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at