chr6-75154447-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS1
The NM_004370.6(COL12A1):c.3534C>T(p.Ser1178=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000062 in 1,611,984 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 (★★). Synonymous variant affecting the same amino acid position (i.e. S1178S) 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 -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL12A1 | NM_004370.6 | c.3534C>T | p.Ser1178= | synonymous_variant | 17/66 | ENST00000322507.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL12A1 | ENST00000322507.13 | c.3534C>T | p.Ser1178= | synonymous_variant | 17/66 | 1 | NM_004370.6 | P4 | |
COL12A1 | ENST00000345356.10 | c.74-1965C>T | intron_variant | 1 | |||||
COL12A1 | ENST00000483888.6 | c.3534C>T | p.Ser1178= | synonymous_variant | 17/65 | 5 | A1 | ||
COL12A1 | ENST00000416123.6 | c.3534C>T | p.Ser1178= | synonymous_variant | 16/63 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000224 AC: 34AN: 152020Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000845 AC: 21AN: 248652Hom.: 0 AF XY: 0.0000667 AC XY: 9AN XY: 134912
GnomAD4 exome AF: 0.0000452 AC: 66AN: 1459964Hom.: 0 Cov.: 30 AF XY: 0.0000385 AC XY: 28AN XY: 726336
GnomAD4 genome AF: 0.000224 AC: 34AN: 152020Hom.: 0 Cov.: 32 AF XY: 0.000229 AC XY: 17AN XY: 74226
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 11, 2020 | - - |
Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 23, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at