14-24336183-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006871.4(RIPK3):c.1549G>A(p.Gly517Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,611,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006871.4 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 |
---|---|---|---|---|---|---|---|---|---|---|
RIPK3 | ENST00000216274.10 | c.1549G>A | p.Gly517Arg | missense_variant | Exon 10 of 10 | 1 | NM_006871.4 | ENSP00000216274.5 | ||
RIPK3 | ENST00000554756.1 | n.*891G>A | non_coding_transcript_exon_variant | Exon 10 of 10 | 1 | ENSP00000452328.1 | ||||
RIPK3 | ENST00000554756.1 | n.*891G>A | 3_prime_UTR_variant | Exon 10 of 10 | 1 | ENSP00000452328.1 | ||||
ENSG00000258973 | ENST00000555591.1 | n.358+702G>A | intron_variant | Intron 2 of 3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250674Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135516
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1459502Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 725814
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1549G>A (p.G517R) alteration is located in exon 10 (coding exon 10) of the RIPK3 gene. This alteration results from a G to A substitution at nucleotide position 1549, causing the glycine (G) at amino acid position 517 to be replaced by an arginine (R). 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