chr17-3008058-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_015085.5(RAP1GAP2):āc.1407C>Gā(p.His469Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000483 in 1,613,820 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. H469H) has been classified as Benign.
Frequency
Consequence
NM_015085.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAP1GAP2 | NM_015085.5 | c.1407C>G | p.His469Gln | missense_variant | 17/25 | ENST00000254695.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAP1GAP2 | ENST00000254695.13 | c.1407C>G | p.His469Gln | missense_variant | 17/25 | 1 | NM_015085.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152168Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461652Hom.: 0 Cov.: 31 AF XY: 0.0000550 AC XY: 40AN XY: 727122
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2022 | The c.1407C>G (p.H469Q) alteration is located in exon 17 (coding exon 17) of the RAP1GAP2 gene. This alteration results from a C to G substitution at nucleotide position 1407, causing the histidine (H) at amino acid position 469 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at