rs149832668
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBS1BS2
The NM_004370.6(COL12A1):c.2480C>T(p.Thr827Met) variant causes a missense change. The variant allele was found at a frequency of 0.000377 in 1,614,084 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T827T) has been classified as Benign.
Frequency
Consequence
NM_004370.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL12A1 | NM_004370.6 | c.2480C>T | p.Thr827Met | missense_variant | 13/66 | ENST00000322507.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL12A1 | ENST00000322507.13 | c.2480C>T | p.Thr827Met | missense_variant | 13/66 | 1 | NM_004370.6 | P4 | |
COL12A1 | ENST00000345356.10 | c.74-22786C>T | intron_variant | 1 | |||||
COL12A1 | ENST00000483888.6 | c.2480C>T | p.Thr827Met | missense_variant | 13/65 | 5 | A1 | ||
COL12A1 | ENST00000416123.6 | c.2480C>T | p.Thr827Met | missense_variant | 12/63 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 152090Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000197 AC: 49AN: 249304Hom.: 1 AF XY: 0.000163 AC XY: 22AN XY: 135242
GnomAD4 exome AF: 0.000396 AC: 579AN: 1461876Hom.: 6 Cov.: 31 AF XY: 0.000388 AC XY: 282AN XY: 727242
GnomAD4 genome ? AF: 0.000191 AC: 29AN: 152208Hom.: 1 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74414
ClinVar
Submissions by phenotype
Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at