17-80374694-A-G
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_001256071.3(RNF213):c.13074+105A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 1,352,698 control chromosomes in the GnomAD database, including 454,532 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).
Frequency
Genomes: 𝑓 0.82 ( 51861 hom., cov: 31)
Exomes 𝑓: 0.82 ( 402671 hom. )
Consequence
RNF213
NM_001256071.3 intron
NM_001256071.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.524
Genes affected
RNF213 (HGNC:14539): (ring finger protein 213) This gene encodes a protein containing a C3HC4-type RING finger domain, which is a specialized type of Zn-finger that binds two atoms of zinc and is thought to be involved in mediating protein-protein interactions. The protein also contains an AAA domain, which is associated with ATPase activity. This gene is a susceptibility gene for Moyamoya disease, a vascular disorder of intracranial arteries. This gene is also a translocation partner in anaplastic large cell lymphoma and inflammatory myofibroblastic tumor cases, where a t(2;17)(p23;q25) translocation has been identified with the anaplastic lymphoma kinase (ALK) gene on chromosome 2, and a t(8;17)(q24;q25) translocation has been identified with the MYC gene on chromosome 8. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
Variant 17-80374694-A-G is Benign according to our data. Variant chr17-80374694-A-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RNF213 | NM_001256071.3 | c.13074+105A>G | intron_variant | ENST00000582970.6 | NP_001243000.2 | |||
RNF213-AS1 | NR_029376.1 | n.241-19406T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RNF213 | ENST00000582970.6 | c.13074+105A>G | intron_variant | 1 | NM_001256071.3 | ENSP00000464087 | P2 | |||
RNF213-AS1 | ENST00000575034.5 | n.191-19406T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.820 AC: 124688AN: 151966Hom.: 51821 Cov.: 31
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GnomAD3 exomes AF: 0.757 AC: 127806AN: 168874Hom.: 49706 AF XY: 0.760 AC XY: 68635AN XY: 90344
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GnomAD4 exome AF: 0.815 AC: 978561AN: 1200614Hom.: 402671 Cov.: 15 AF XY: 0.812 AC XY: 488864AN XY: 602218
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GnomAD4 genome AF: 0.820 AC: 124769AN: 152084Hom.: 51861 Cov.: 31 AF XY: 0.811 AC XY: 60301AN XY: 74332
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at