chr17-2965594-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_015085.5(RAP1GAP2):c.547G>A(p.Val183Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000577 in 1,612,688 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_015085.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAP1GAP2 | NM_015085.5 | c.547G>A | p.Val183Ile | missense_variant | 8/25 | ENST00000254695.13 | |
LOC101927911 | NR_110818.1 | n.302C>T | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAP1GAP2 | ENST00000254695.13 | c.547G>A | p.Val183Ile | missense_variant | 8/25 | 1 | NM_015085.5 | P4 | |
ENST00000574885.1 | n.302C>T | non_coding_transcript_exon_variant | 1/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000224 AC: 34AN: 152084Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000526 AC: 13AN: 247086Hom.: 0 AF XY: 0.0000522 AC XY: 7AN XY: 134046
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1460486Hom.: 0 Cov.: 30 AF XY: 0.0000372 AC XY: 27AN XY: 726384
GnomAD4 genome AF: 0.000223 AC: 34AN: 152202Hom.: 0 Cov.: 31 AF XY: 0.000161 AC XY: 12AN XY: 74422
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at