8-89769803-T-C
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003821.6(RIPK2):c.515T>C(p.Met172Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000529 in 1,606,186 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M172V) has been classified as Uncertain significance.
Frequency
Consequence
NM_003821.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Our verdict: Likely_benign. The variant received -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RIPK2 | NM_003821.6 | c.515T>C | p.Met172Thr | missense_variant | Exon 4 of 11 | ENST00000220751.5 | NP_003812.1 | |
RIPK2 | XM_011517357.3 | c.2T>C | p.Met1? | start_lost | Exon 2 of 9 | XP_011515659.1 | ||
RIPK2 | NM_001375360.1 | c.104T>C | p.Met35Thr | missense_variant | Exon 3 of 10 | NP_001362289.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RIPK2 | ENST00000220751.5 | c.515T>C | p.Met172Thr | missense_variant | Exon 4 of 11 | 1 | NM_003821.6 | ENSP00000220751.4 | ||
RIPK2 | ENST00000522965.1 | n.*154T>C | non_coding_transcript_exon_variant | Exon 3 of 10 | 1 | ENSP00000429271.1 | ||||
RIPK2 | ENST00000522965.1 | n.*154T>C | 3_prime_UTR_variant | Exon 3 of 10 | 1 | ENSP00000429271.1 |
Frequencies
GnomAD3 genomes AF: 0.0000790 AC: 12AN: 151910Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000612 AC: 15AN: 245098 AF XY: 0.0000753 show subpopulations
GnomAD4 exome AF: 0.0000502 AC: 73AN: 1454158Hom.: 0 Cov.: 31 AF XY: 0.0000525 AC XY: 38AN XY: 723406 show subpopulations
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152028Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74334 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.515T>C (p.M172T) alteration is located in exon 4 (coding exon 4) of the RIPK2 gene. This alteration results from a T to C substitution at nucleotide position 515, causing the methionine (M) at amino acid position 172 to be replaced by a threonine (T). 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