2-112388348-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001164463.1(RGPD8):c.4597G>A(p.Val1533Ile) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001164463.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RGPD8 | ENST00000302558.8 | c.4597G>A | p.Val1533Ile | missense_variant | Exon 20 of 23 | 1 | NM_001164463.1 | ENSP00000306637.3 | ||
RGPD8 | ENST00000409750.5 | c.4177G>A | p.Val1393Ile | missense_variant | Exon 19 of 22 | 1 | ENSP00000386511.1 |
Frequencies
GnomAD3 genomes AF: 0.0000102 AC: 1AN: 98366Hom.: 0 Cov.: 13
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000573 AC: 8AN: 1397282Hom.: 0 Cov.: 33 AF XY: 0.00000574 AC XY: 4AN XY: 696560
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000102 AC: 1AN: 98366Hom.: 0 Cov.: 13 AF XY: 0.00 AC XY: 0AN XY: 46388
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4597G>A (p.V1533I) alteration is located in exon 20 (coding exon 20) of the RGPD8 gene. This alteration results from a G to A substitution at nucleotide position 4597, causing the valine (V) at amino acid position 1533 to be replaced by an isoleucine (I). 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