rs397514563
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 9P and 1B. PS1_ModeratePM1PM2PP2PP5_ModerateBP4
The NM_001256071.3(RNF213):c.12037G>A(p.Asp4013Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,614,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_001256071.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF213 | NM_001256071.3 | c.12037G>A | p.Asp4013Asn | missense_variant | 44/68 | ENST00000582970.6 | |
RNF213-AS1 | NR_029376.1 | n.241-12737C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF213 | ENST00000582970.6 | c.12037G>A | p.Asp4013Asn | missense_variant | 44/68 | 1 | NM_001256071.3 | P2 | |
RNF213-AS1 | ENST00000575034.5 | n.191-12737C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251452Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135902
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727244
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74372
ClinVar
Submissions by phenotype
Moyamoya disease 2 Pathogenic:3Other:1
Pathogenic, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Likely pathogenic, no assertion criteria provided | research | UMR-S1161, Institut national de la santé et de la recherche médicale | Mar 03, 2017 | - - |
Likely pathogenic, no assertion criteria provided | research | Department of Internal Medicine, University of Texas Health Science Center at Houston | Sep 08, 2014 | - - |
risk factor, no assertion criteria provided | literature only | OMIM | Jan 01, 2011 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at