rs2013109
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002934.3(RNASE2):c.-6+95G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 1,127,990 control chromosomes in the GnomAD database, including 36,899 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 0.20 ( 3595 hom., cov: 32)
Exomes 𝑓: 0.26 ( 33304 hom. )
Consequence
RNASE2
NM_002934.3 intron
NM_002934.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.137
Genes affected
RNASE2 (HGNC:10045): (ribonuclease A family member 2) The protein encoded by this gene is a non-secretory ribonuclease that belongs to the pancreatic ribonuclease family, a subset of the ribonuclease A superfamily. The protein antimicrobial activity against viruses. [provided by RefSeq, Oct 2014]
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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=-0.92).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNASE2 | NM_002934.3 | c.-6+95G>C | intron_variant | ENST00000304625.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNASE2 | ENST00000304625.3 | c.-6+95G>C | intron_variant | 1 | NM_002934.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.201 AC: 30610AN: 151988Hom.: 3595 Cov.: 32
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GnomAD4 exome AF: 0.256 AC: 250248AN: 975884Hom.: 33304 Cov.: 13 AF XY: 0.258 AC XY: 126989AN XY: 492384
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GnomAD4 genome ? AF: 0.201 AC: 30612AN: 152106Hom.: 3595 Cov.: 32 AF XY: 0.203 AC XY: 15070AN XY: 74338
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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