rs147021687
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_032193.4(RNASEH2C):āc.417C>Gā(p.Gly139Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00141 in 1,614,208 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_032193.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RNASEH2C | NM_032193.4 | c.417C>G | p.Gly139Gly | synonymous_variant | Exon 3 of 4 | ENST00000308418.10 | NP_115569.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00215 AC: 327AN: 152246Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00241 AC: 606AN: 251384Hom.: 8 AF XY: 0.00234 AC XY: 318AN XY: 135890
GnomAD4 exome AF: 0.00133 AC: 1948AN: 1461844Hom.: 13 Cov.: 32 AF XY: 0.00134 AC XY: 976AN XY: 727224
GnomAD4 genome AF: 0.00215 AC: 327AN: 152364Hom.: 3 Cov.: 32 AF XY: 0.00264 AC XY: 197AN XY: 74512
ClinVar
Submissions by phenotype
Aicardi-Goutieres syndrome 3 Uncertain:1Benign:3
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
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not provided Benign:1
RNASEH2C: BP4, BP7, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at