chr1-92323785-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_024813.3(RPAP2):c.865G>A(p.Glu289Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000878 in 1,614,026 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024813.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPAP2 | NM_024813.3 | c.865G>A | p.Glu289Lys | missense_variant | 8/13 | ENST00000610020.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPAP2 | ENST00000610020.2 | c.865G>A | p.Glu289Lys | missense_variant | 8/13 | 1 | NM_024813.3 | P1 | |
RPAP2 | ENST00000484158.1 | n.739G>A | non_coding_transcript_exon_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000585 AC: 89AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000531 AC: 133AN: 250548Hom.: 0 AF XY: 0.000517 AC XY: 70AN XY: 135482
GnomAD4 exome AF: 0.000909 AC: 1328AN: 1461696Hom.: 2 Cov.: 32 AF XY: 0.000840 AC XY: 611AN XY: 727152
GnomAD4 genome ? AF: 0.000584 AC: 89AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.000510 AC XY: 38AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 09, 2021 | The c.865G>A (p.E289K) alteration is located in exon 8 (coding exon 8) of the RPAP2 gene. This alteration results from a G to A substitution at nucleotide position 865, causing the glutamic acid (E) at amino acid position 289 to be replaced by a lysine (K). 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