rs75535959
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_004370.6(COL12A1):āc.626A>Cā(p.Lys209Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0042 in 1,613,054 control chromosomes in the GnomAD database, including 239 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_004370.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL12A1 | NM_004370.6 | c.626A>C | p.Lys209Thr | missense_variant | 6/66 | ENST00000322507.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL12A1 | ENST00000322507.13 | c.626A>C | p.Lys209Thr | missense_variant | 6/66 | 1 | NM_004370.6 | P4 | |
COL12A1 | ENST00000345356.10 | c.73+13136A>C | intron_variant | 1 | |||||
COL12A1 | ENST00000483888.6 | c.626A>C | p.Lys209Thr | missense_variant | 6/65 | 5 | A1 | ||
COL12A1 | ENST00000416123.6 | c.626A>C | p.Lys209Thr | missense_variant | 5/63 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0224 AC: 3414AN: 152078Hom.: 112 Cov.: 32
GnomAD3 exomes AF: 0.00565 AC: 1395AN: 246950Hom.: 40 AF XY: 0.00449 AC XY: 602AN XY: 134190
GnomAD4 exome AF: 0.00230 AC: 3361AN: 1460858Hom.: 127 Cov.: 32 AF XY: 0.00198 AC XY: 1439AN XY: 726696
GnomAD4 genome ? AF: 0.0225 AC: 3421AN: 152196Hom.: 112 Cov.: 32 AF XY: 0.0212 AC XY: 1580AN XY: 74428
ClinVar
Submissions by phenotype
Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 24, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 07, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at