15-41520684-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_015540.4(RPAP1):c.3502G>A(p.Glu1168Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000682 in 1,614,024 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 Uncertain significance (★).
Frequency
Consequence
NM_015540.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPAP1 | NM_015540.4 | c.3502G>A | p.Glu1168Lys | missense_variant | Exon 22 of 25 | ENST00000304330.9 | NP_056355.2 | |
RPAP1 | XM_005254297.2 | c.3502G>A | p.Glu1168Lys | missense_variant | Exon 22 of 25 | XP_005254354.1 | ||
RPAP1 | XM_047432374.1 | c.3322G>A | p.Glu1108Lys | missense_variant | Exon 21 of 24 | XP_047288330.1 | ||
RPAP1 | XM_047432375.1 | c.3322G>A | p.Glu1108Lys | missense_variant | Exon 21 of 24 | XP_047288331.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPAP1 | ENST00000304330.9 | c.3502G>A | p.Glu1168Lys | missense_variant | Exon 22 of 25 | 1 | NM_015540.4 | ENSP00000306123.4 | ||
RPAP1 | ENST00000562303.5 | n.3502G>A | non_coding_transcript_exon_variant | Exon 22 of 24 | 1 | ENSP00000455363.1 | ||||
RPAP1 | ENST00000565167.1 | n.518G>A | non_coding_transcript_exon_variant | Exon 2 of 4 | 1 | |||||
RPAP1 | ENST00000561603.5 | c.3038+1054G>A | intron_variant | Intron 21 of 23 | 5 | ENSP00000456207.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251220Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135816
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461824Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727218
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3502G>A (p.E1168K) alteration is located in exon 22 (coding exon 21) of the RPAP1 gene. This alteration results from a G to A substitution at nucleotide position 3502, causing the glutamic acid (E) at amino acid position 1168 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