chr6-75119098-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004370.6(COL12A1):c.7299G>T(p.Thr2433=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00271 in 1,613,942 control chromosomes in the GnomAD database, including 80 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T2433T) has been classified as Likely benign.
Frequency
Consequence
NM_004370.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL12A1 | NM_004370.6 | c.7299G>T | p.Thr2433= | synonymous_variant | 46/66 | ENST00000322507.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL12A1 | ENST00000322507.13 | c.7299G>T | p.Thr2433= | synonymous_variant | 46/66 | 1 | NM_004370.6 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0128 AC: 1949AN: 152120Hom.: 41 Cov.: 33
GnomAD3 exomes AF: 0.00392 AC: 977AN: 249376Hom.: 22 AF XY: 0.00299 AC XY: 405AN XY: 135282
GnomAD4 exome AF: 0.00166 AC: 2431AN: 1461704Hom.: 39 Cov.: 31 AF XY: 0.00145 AC XY: 1051AN XY: 727154
GnomAD4 genome AF: 0.0128 AC: 1945AN: 152238Hom.: 41 Cov.: 33 AF XY: 0.0123 AC XY: 916AN XY: 74426
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 | Oct 11, 2018 | - - |
Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at