6-24809708-A-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001286445.3(RIPOR2):c.3043+9T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,517,870 control chromosomes in the GnomAD database, including 15,470 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.12 ( 1314 hom., cov: 32)
Exomes 𝑓: 0.14 ( 14156 hom. )
Consequence
RIPOR2
NM_001286445.3 intron
NM_001286445.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.338
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
Variant 6-24809708-A-T is Benign according to our data. Variant chr6-24809708-A-T is described in ClinVar as [Benign]. Clinvar id is 517553.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RIPOR2 | NM_001286445.3 | c.3043+9T>A | intron_variant | ENST00000643898.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIPOR2 | ENST00000643898.2 | c.3043+9T>A | intron_variant | NM_001286445.3 | A2 | ||||
RIPOR2 | ENST00000259698.9 | c.3106+9T>A | intron_variant | 1 | A2 | ||||
RIPOR2 | ENST00000538035.6 | c.2956+9T>A | intron_variant | 2 | A2 | ||||
RIPOR2 | ENST00000613507.4 | c.3106+9T>A | intron_variant | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.124 AC: 18902AN: 152104Hom.: 1312 Cov.: 32
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GnomAD3 exomes AF: 0.140 AC: 21907AN: 156336Hom.: 1639 AF XY: 0.139 AC XY: 11508AN XY: 82862
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GnomAD4 exome AF: 0.142 AC: 193750AN: 1365652Hom.: 14156 Cov.: 25 AF XY: 0.141 AC XY: 95378AN XY: 675634
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GnomAD4 genome AF: 0.124 AC: 18911AN: 152218Hom.: 1314 Cov.: 32 AF XY: 0.125 AC XY: 9303AN XY: 74410
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 23, 2017 | c.3106+9T>A in intron 22 of FAM65B: This variant is not expected to have clinica l significance because it does not alter an amino acid residue, is not located w ithin the splice consensus sequence, and has been identified in 15.70% (255/1624 ) of Finnish chromosomes by the Exome Aggregation Consortium (ExAC, http://exac. broadinstitute.org; dbSNP rs9379693). - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 09, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Autosomal recessive nonsyndromic hearing loss 104 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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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