2-203439630-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_213589.3(RAPH1):c.3560G>A(p.Arg1187His) variant causes a missense change. The variant allele was found at a frequency of 0.0000774 in 1,614,010 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 (★).
Frequency
Consequence
NM_213589.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152038Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 250950Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135728
GnomAD4 exome AF: 0.0000821 AC: 120AN: 1461854Hom.: 0 Cov.: 34 AF XY: 0.0000935 AC XY: 68AN XY: 727222
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152156Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74402
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3560G>A (p.R1187H) alteration is located in exon 14 (coding exon 13) of the RAPH1 gene. This alteration results from a G to A substitution at nucleotide position 3560, causing the arginine (R) at amino acid position 1187 to be replaced by a histidine (H). 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