chr3-33114093-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_006371.5(CRTAP):c.16C>A(p.Arg6=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000763 in 1,310,866 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). Synonymous variant affecting the same amino acid position (i.e. R6R) has been classified as Likely benign.
Frequency
Consequence
NM_006371.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRTAP | NM_006371.5 | c.16C>A | p.Arg6= | synonymous_variant | 1/7 | ENST00000320954.11 | |
CRTAP | NM_001393363.1 | c.16C>A | p.Arg6= | synonymous_variant | 1/6 | ||
CRTAP | NM_001393364.1 | c.16C>A | p.Arg6= | synonymous_variant | 1/6 | ||
CRTAP | NM_001393365.1 | c.16C>A | p.Arg6= | synonymous_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRTAP | ENST00000320954.11 | c.16C>A | p.Arg6= | synonymous_variant | 1/7 | 1 | NM_006371.5 | P1 | |
CRTAP | ENST00000449224.1 | c.16C>A | p.Arg6= | synonymous_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome AF: 7.63e-7 AC: 1AN: 1310866Hom.: 0 Cov.: 31 AF XY: 0.00000155 AC XY: 1AN XY: 647122
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Osteogenesis imperfecta Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Dec 01, 2018 | - - |
Osteogenesis imperfecta type 7 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 16, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.