6-75087586-C-T
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004370.6(COL12A1):c.9172G>A(p.Gly3058Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.76 in 1,613,022 control chromosomes in the GnomAD database, including 468,079 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G3058N) has been classified as Uncertain significance.
Frequency
Consequence
NM_004370.6 missense
Scores
Clinical Significance
Conservation
Publications
- Bethlem myopathy 2Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
- Bethlem myopathy 2Inheritance: AD Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Illumina, Genomics England PanelApp
- Ullrich congenital muscular dystrophy 2Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- Bethlem myopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Ullrich congenital muscular dystrophyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.726 AC: 110227AN: 151856Hom.: 40303 Cov.: 30 show subpopulations
GnomAD2 exomes AF: 0.747 AC: 185847AN: 248804 AF XY: 0.741 show subpopulations
GnomAD4 exome AF: 0.764 AC: 1115636AN: 1461048Hom.: 427763 Cov.: 56 AF XY: 0.761 AC XY: 552931AN XY: 726870 show subpopulations
GnomAD4 genome AF: 0.726 AC: 110286AN: 151974Hom.: 40316 Cov.: 30 AF XY: 0.718 AC XY: 53347AN XY: 74264 show subpopulations
ClinVar
Submissions by phenotype
not specified Benign:3
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Bethlem myopathy 2 Benign:1
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not provided Benign:1
This variant is associated with the following publications: (PMID: 16741161) -
Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2 Benign:1
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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