6-75128355-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004370.6(COL12A1):c.6281C>A(p.Thr2094Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000214 in 1,610,148 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_004370.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL12A1 | ENST00000322507.13 | c.6281C>A | p.Thr2094Asn | missense_variant | Exon 38 of 66 | 1 | NM_004370.6 | ENSP00000325146.8 | ||
COL12A1 | ENST00000345356.10 | c.2789C>A | p.Thr930Asn | missense_variant | Exon 23 of 51 | 1 | ENSP00000305147.9 | |||
COL12A1 | ENST00000483888.6 | c.6281C>A | p.Thr2094Asn | missense_variant | Exon 38 of 65 | 5 | ENSP00000421216.1 | |||
COL12A1 | ENST00000416123.6 | c.6281C>A | p.Thr2094Asn | missense_variant | Exon 37 of 63 | 5 | ENSP00000412864.2 |
Frequencies
GnomAD3 genomes AF: 0.000414 AC: 63AN: 152110Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000897 AC: 221AN: 246326Hom.: 3 AF XY: 0.000875 AC XY: 117AN XY: 133698
GnomAD4 exome AF: 0.000193 AC: 282AN: 1457920Hom.: 2 Cov.: 30 AF XY: 0.000193 AC XY: 140AN XY: 725168
GnomAD4 genome AF: 0.000407 AC: 62AN: 152228Hom.: 1 Cov.: 32 AF XY: 0.000524 AC XY: 39AN XY: 74418
ClinVar
Submissions by phenotype
COL12A1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at