6-75181206-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP2BP4_StrongBP6BS1
The NM_004370.6(COL12A1):c.1897G>T(p.Val633Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00028 in 1,507,156 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V633I) has been classified as Uncertain significance.
Frequency
Consequence
NM_004370.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL12A1 | NM_004370.6 | c.1897G>T | p.Val633Phe | missense_variant | 11/66 | ENST00000322507.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL12A1 | ENST00000322507.13 | c.1897G>T | p.Val633Phe | missense_variant | 11/66 | 1 | NM_004370.6 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00251 AC: 215AN: 85518Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000447 AC: 88AN: 196792Hom.: 0 AF XY: 0.000295 AC XY: 32AN XY: 108634
GnomAD4 exome AF: 0.000146 AC: 207AN: 1421554Hom.: 0 Cov.: 31 AF XY: 0.000103 AC XY: 73AN XY: 706022
GnomAD4 genome AF: 0.00251 AC: 215AN: 85602Hom.: 0 Cov.: 31 AF XY: 0.00246 AC XY: 100AN XY: 40718
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 08, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Aug 12, 2021 | - - |
Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at