chr17-80287950-C-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_001256071.3(RNF213):c.397C>A(p.Leu133Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00173 in 1,570,594 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001256071.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF213 | NM_001256071.3 | c.397C>A | p.Leu133Met | missense_variant | 4/68 | ENST00000582970.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF213 | ENST00000582970.6 | c.397C>A | p.Leu133Met | missense_variant | 4/68 | 1 | NM_001256071.3 | P2 | |
RNF213 | ENST00000319921.4 | c.397C>A | p.Leu133Met | missense_variant | 4/17 | 1 | |||
RNF213 | ENST00000508628.6 | c.544C>A | p.Leu182Met | missense_variant | 5/69 | 5 | A2 | ||
RNF213 | ENST00000559070.5 | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.000939 AC: 143AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00102 AC: 185AN: 180754Hom.: 1 AF XY: 0.000971 AC XY: 94AN XY: 96780
GnomAD4 exome AF: 0.00182 AC: 2575AN: 1418266Hom.: 2 Cov.: 34 AF XY: 0.00175 AC XY: 1230AN XY: 701976
GnomAD4 genome AF: 0.000939 AC: 143AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.000926 AC XY: 69AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | RNF213: BP4, BS2 - |
Moyamoya disease 2 Uncertain:1
Uncertain significance, no assertion criteria provided | research | UMR-S1161, Institut national de la santé et de la recherche médicale | Mar 03, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at