chr3-33114095-G-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_006371.5(CRTAP):c.18G>C(p.Arg6=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000546 in 1,464,488 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. 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 Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRTAP | NM_006371.5 | c.18G>C | p.Arg6= | synonymous_variant | 1/7 | ENST00000320954.11 | |
CRTAP | NM_001393363.1 | c.18G>C | p.Arg6= | synonymous_variant | 1/6 | ||
CRTAP | NM_001393364.1 | c.18G>C | p.Arg6= | synonymous_variant | 1/6 | ||
CRTAP | NM_001393365.1 | c.18G>C | p.Arg6= | synonymous_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRTAP | ENST00000320954.11 | c.18G>C | p.Arg6= | synonymous_variant | 1/7 | 1 | NM_006371.5 | P1 | |
CRTAP | ENST00000449224.1 | c.18G>C | p.Arg6= | synonymous_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151978Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000267 AC: 2AN: 74990Hom.: 0 AF XY: 0.0000456 AC XY: 2AN XY: 43820
GnomAD4 exome AF: 0.00000533 AC: 7AN: 1312510Hom.: 0 Cov.: 32 AF XY: 0.00000463 AC XY: 3AN XY: 648042
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151978Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74252
ClinVar
Submissions by phenotype
Osteogenesis imperfecta type 7 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 06, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Mar 02, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at