8-89772777-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003821.6(RIPK2):āc.802C>Gā(p.Leu268Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00133 in 1,610,338 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003821.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RIPK2 | NM_003821.6 | c.802C>G | p.Leu268Val | missense_variant | 6/11 | ENST00000220751.5 | |
RIPK2 | NM_001375360.1 | c.391C>G | p.Leu131Val | missense_variant | 5/10 | ||
RIPK2 | XM_011517357.3 | c.289C>G | p.Leu97Val | missense_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIPK2 | ENST00000220751.5 | c.802C>G | p.Leu268Val | missense_variant | 6/11 | 1 | NM_003821.6 | P1 | |
RIPK2 | ENST00000522965.1 | c.*441C>G | 3_prime_UTR_variant, NMD_transcript_variant | 5/10 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00736 AC: 1118AN: 151968Hom.: 12 Cov.: 32
GnomAD3 exomes AF: 0.00183 AC: 456AN: 248534Hom.: 6 AF XY: 0.00133 AC XY: 179AN XY: 134332
GnomAD4 exome AF: 0.000704 AC: 1027AN: 1458252Hom.: 16 Cov.: 29 AF XY: 0.000608 AC XY: 441AN XY: 725364
GnomAD4 genome AF: 0.00736 AC: 1119AN: 152086Hom.: 12 Cov.: 32 AF XY: 0.00683 AC XY: 508AN XY: 74380
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 26, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at