chr14-20956082-A-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002934.3(RNASE2):c.311A>C(p.Gln104Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000642 in 1,614,252 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002934.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNASE2 | NM_002934.3 | c.311A>C | p.Gln104Pro | missense_variant | 2/2 | ENST00000304625.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNASE2 | ENST00000304625.3 | c.311A>C | p.Gln104Pro | missense_variant | 2/2 | 1 | NM_002934.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000578 AC: 88AN: 152242Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00124 AC: 312AN: 251454Hom.: 6 AF XY: 0.00146 AC XY: 199AN XY: 135894
GnomAD4 exome AF: 0.000648 AC: 948AN: 1461892Hom.: 11 Cov.: 31 AF XY: 0.000811 AC XY: 590AN XY: 727246
GnomAD4 genome ? AF: 0.000578 AC: 88AN: 152360Hom.: 1 Cov.: 32 AF XY: 0.000631 AC XY: 47AN XY: 74512
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 12, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at