rs553076085
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_006371.5(CRTAP):c.88C>A(p.Arg30Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,588,854 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 Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R30C) has been classified as Uncertain significance.
Frequency
Consequence
NM_006371.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRTAP | NM_006371.5 | c.88C>A | p.Arg30Ser | missense_variant | 1/7 | ENST00000320954.11 | |
CRTAP | NM_001393363.1 | c.88C>A | p.Arg30Ser | missense_variant | 1/6 | ||
CRTAP | NM_001393364.1 | c.88C>A | p.Arg30Ser | missense_variant | 1/6 | ||
CRTAP | NM_001393365.1 | c.88C>A | p.Arg30Ser | missense_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRTAP | ENST00000320954.11 | c.88C>A | p.Arg30Ser | missense_variant | 1/7 | 1 | NM_006371.5 | P1 | |
CRTAP | ENST00000449224.1 | c.88C>A | p.Arg30Ser | missense_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152078Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000195 AC: 41AN: 209998Hom.: 0 AF XY: 0.000281 AC XY: 33AN XY: 117644
GnomAD4 exome AF: 0.000116 AC: 166AN: 1436668Hom.: 1 Cov.: 32 AF XY: 0.000152 AC XY: 109AN XY: 715052
GnomAD4 genome ? AF: 0.0000789 AC: 12AN: 152186Hom.: 0 Cov.: 34 AF XY: 0.0000672 AC XY: 5AN XY: 74404
ClinVar
Submissions by phenotype
Osteogenesis imperfecta type 7 Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 24, 2022 | This sequence change replaces arginine, which is basic and polar, with serine, which is neutral and polar, at codon 30 of the CRTAP protein (p.Arg30Ser). This variant is present in population databases (rs553076085, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with CRTAP-related conditions. ClinVar contains an entry for this variant (Variation ID: 581625). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Nov 08, 2019 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at