6-75086552-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_004370.6(COL12A1):c.9187G>A(p.Gly3063Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000437 in 1,600,800 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004370.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000330 AC: 5AN: 151466Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000404 AC: 10AN: 247722Hom.: 1 AF XY: 0.0000595 AC XY: 8AN XY: 134478
GnomAD4 exome AF: 0.0000448 AC: 65AN: 1449334Hom.: 1 Cov.: 29 AF XY: 0.0000471 AC XY: 34AN XY: 721340
GnomAD4 genome AF: 0.0000330 AC: 5AN: 151466Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 73914
ClinVar
Submissions by phenotype
not provided Uncertain:2
Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant does not alter protein structure/function -
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Inborn genetic diseases Uncertain:1
The c.9187G>A (p.G3063S) alteration is located in exon 66 (coding exon 65) of the COL12A1 gene. This alteration results from a G to A substitution at nucleotide position 9187, causing the glycine (G) at amino acid position 3063 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
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