2-27377416-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144631.6(ZNF513):c.*129G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000775 in 1,026,952 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_144631.6 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF513 | ENST00000323703 | c.*129G>A | 3_prime_UTR_variant | Exon 4 of 4 | 1 | NM_144631.6 | ENSP00000318373.6 | |||
SNX17 | ENST00000233575.7 | c.*697C>T | 3_prime_UTR_variant | Exon 15 of 15 | 1 | NM_014748.4 | ENSP00000233575.2 | |||
ZNF513 | ENST00000407879 | c.*129G>A | 3_prime_UTR_variant | Exon 3 of 3 | 1 | ENSP00000384874.1 | ||||
SNX17 | ENST00000537606.5 | c.*697C>T | 3_prime_UTR_variant | Exon 14 of 14 | 2 | ENSP00000439208.1 |
Frequencies
GnomAD3 genomes AF: 0.000467 AC: 71AN: 152146Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000509 AC: 75AN: 147456Hom.: 1 AF XY: 0.000560 AC XY: 45AN XY: 80378
GnomAD4 exome AF: 0.000829 AC: 725AN: 874688Hom.: 1 Cov.: 12 AF XY: 0.000813 AC XY: 367AN XY: 451576
GnomAD4 genome AF: 0.000466 AC: 71AN: 152264Hom.: 0 Cov.: 33 AF XY: 0.000484 AC XY: 36AN XY: 74454
ClinVar
Submissions by phenotype
not provided Uncertain:1
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Retinitis Pigmentosa, Dominant Uncertain:1
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Retinitis pigmentosa Uncertain: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, 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at