rs75574668
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_001286445.3(RIPOR2):c.1858-1486C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00598 in 1,535,374 control chromosomes in the GnomAD database, including 223 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.022 ( 124 hom., cov: 31)
Exomes 𝑓: 0.0042 ( 99 hom. )
Consequence
RIPOR2
NM_001286445.3 intron
NM_001286445.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.914
Genes affected
RIPOR2 (HGNC:13872): (RHO family interacting cell polarization regulator 2) This gene encodes an atypical inhibitor of the small G protein RhoA. Inhibition of RhoA activity by the encoded protein mediates myoblast fusion and polarization of T cells and neutrophils. The encoded protein is a component of hair cell stereocilia that is essential for hearing. A splice site mutation in this gene results in hearing loss in human patients. [provided by RefSeq, Sep 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
?
Variant 6-24840758-G-A is Benign according to our data. Variant chr6-24840758-G-A is described in ClinVar as [Benign]. Clinvar id is 586405.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0698 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RIPOR2 | NM_001286445.3 | c.1858-1486C>T | intron_variant | ENST00000643898.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIPOR2 | ENST00000643898.2 | c.1858-1486C>T | intron_variant | NM_001286445.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0218 AC: 3312AN: 152108Hom.: 122 Cov.: 31
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GnomAD3 exomes AF: 0.00560 AC: 719AN: 128374Hom.: 11 AF XY: 0.00509 AC XY: 358AN XY: 70306
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GnomAD4 exome AF: 0.00424 AC: 5869AN: 1383148Hom.: 99 Cov.: 31 AF XY: 0.00394 AC XY: 2686AN XY: 682496
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GnomAD4 genome ? AF: 0.0218 AC: 3319AN: 152226Hom.: 124 Cov.: 31 AF XY: 0.0203 AC XY: 1514AN XY: 74432
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 01, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 24, 2018 | - - |
Computational 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