12-68652046-G-A
Variant summary
Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PS1PM1PM2PP3_StrongPP5
The NM_001010942.3(RAP1B):c.178G>A(p.Gly60Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,348 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 13/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin ClinVar.
Frequency
Consequence
NM_001010942.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAP1B | NM_001010942.3 | c.178G>A | p.Gly60Arg | missense_variant | 4/8 | ENST00000250559.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAP1B | ENST00000250559.14 | c.178G>A | p.Gly60Arg | missense_variant | 4/8 | 1 | NM_001010942.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459348Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 726008
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Thrombocytopenia 11 with multiple congenital anomalies and dysmorphic facies Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 06, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.