chr3-33114497-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_006371.5(CRTAP):c.420G>T(p.Ala140=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,451,414 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A140A) 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 -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRTAP | NM_006371.5 | c.420G>T | p.Ala140= | synonymous_variant | 1/7 | ENST00000320954.11 | |
CRTAP | NM_001393363.1 | c.420G>T | p.Ala140= | synonymous_variant | 1/6 | ||
CRTAP | NM_001393364.1 | c.420G>T | p.Ala140= | synonymous_variant | 1/6 | ||
CRTAP | NM_001393365.1 | c.420G>T | p.Ala140= | synonymous_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRTAP | ENST00000320954.11 | c.420G>T | p.Ala140= | synonymous_variant | 1/7 | 1 | NM_006371.5 | P1 | |
CRTAP | ENST00000449224.1 | c.420G>T | p.Ala140= | synonymous_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.00000455 AC: 1AN: 219570Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 121556
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1451414Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 721274
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Osteogenesis imperfecta type 7 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 16, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at