11-65717866-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_032193.4(RNASEH2C):c.*1917T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,350 control chromosomes in the GnomAD database, including 11,067 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_032193.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RNASEH2C | NM_032193.4 | c.*1917T>C | 3_prime_UTR_variant | Exon 4 of 4 | ENST00000308418.10 | NP_115569.2 | ||
KAT5 | NM_182710.3 | c.1265-724A>G | intron_variant | Intron 10 of 12 | ENST00000341318.9 | NP_874369.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.374 AC: 56822AN: 151912Hom.: 11048 Cov.: 31
GnomAD4 exome AF: 0.340 AC: 108AN: 318Hom.: 20 Cov.: 0 AF XY: 0.383 AC XY: 69AN XY: 180
GnomAD4 genome AF: 0.374 AC: 56860AN: 152032Hom.: 11047 Cov.: 31 AF XY: 0.366 AC XY: 27186AN XY: 74324
ClinVar
Submissions by phenotype
Aicardi-Goutieres syndrome 3 Benign:1
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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at