rs310237
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001366165.2(RAVER2):c.1929+5905G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0105 in 152,212 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.011 ( 33 hom., cov: 32)
Consequence
RAVER2
NM_001366165.2 intron
NM_001366165.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.91
Genes affected
RAVER2 (HGNC:25577): (ribonucleoprotein, PTB binding 2) Enables RNA binding activity. Predicted to be involved in regulation of alternative mRNA splicing, via spliceosome. Predicted to be located in cytoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0105 (1600/152212) while in subpopulation AFR AF= 0.0364 (1513/41536). AF 95% confidence interval is 0.0349. There are 33 homozygotes in gnomad4. There are 717 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 33 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAVER2 | NM_001366165.2 | c.1929+5905G>A | intron_variant | ENST00000294428.8 | |||
RAVER2 | NM_018211.4 | c.1890+5905G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAVER2 | ENST00000294428.8 | c.1929+5905G>A | intron_variant | 5 | NM_001366165.2 | A2 | |||
RAVER2 | ENST00000371072.8 | c.1890+5905G>A | intron_variant | 1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0105 AC: 1597AN: 152094Hom.: 33 Cov.: 32
GnomAD3 genomes
?
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0105 AC: 1600AN: 152212Hom.: 33 Cov.: 32 AF XY: 0.00964 AC XY: 717AN XY: 74410
GnomAD4 genome
?
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1600
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32
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717
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74410
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10
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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