21-41766883-C-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_ModerateBP6_ModerateBP7BS1
The NM_020639.3(RIPK4):c.159G>T(p.Ser53=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,609,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S53S) has been classified as Benign.
Frequency
Consequence
NM_020639.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RIPK4 | NM_020639.3 | c.159G>T | p.Ser53= | synonymous_variant | 1/8 | ENST00000332512.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIPK4 | ENST00000332512.8 | c.159G>T | p.Ser53= | synonymous_variant | 1/8 | 1 | NM_020639.3 | P1 | |
RIPK4 | ENST00000352483.3 | c.159G>T | p.Ser53= | synonymous_variant | 1/9 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000724 AC: 11AN: 151964Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000292 AC: 7AN: 239656Hom.: 0 AF XY: 0.0000228 AC XY: 3AN XY: 131546
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1457796Hom.: 0 Cov.: 33 AF XY: 0.0000110 AC XY: 8AN XY: 725190
GnomAD4 genome AF: 0.0000724 AC: 11AN: 151964Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74240
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at