X-47977683-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001007088.2(ZNF182):c.347G>A(p.Arg116His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000215 in 1,209,210 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001007088.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF182 | NM_001007088.2 | c.347G>A | p.Arg116His | missense_variant | Exon 6 of 6 | ENST00000376943.8 | NP_001007089.1 | |
ZNF182 | NM_001178099.2 | c.404G>A | p.Arg135His | missense_variant | Exon 7 of 7 | NP_001171570.1 | ||
ZNF182 | NM_006962.2 | c.404G>A | p.Arg135His | missense_variant | Exon 7 of 7 | NP_008893.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF182 | ENST00000376943.8 | c.347G>A | p.Arg116His | missense_variant | Exon 6 of 6 | 1 | NM_001007088.2 | ENSP00000366142.4 | ||
ZNF182 | ENST00000396965.5 | c.404G>A | p.Arg135His | missense_variant | Exon 7 of 7 | 2 | ENSP00000380165.1 | |||
ZNF81 | ENST00000376950.4 | c.278-24845C>T | intron_variant | Intron 4 of 4 | 5 | ENSP00000366149.4 |
Frequencies
GnomAD3 genomes AF: 0.000107 AC: 12AN: 112225Hom.: 0 Cov.: 23 AF XY: 0.0000872 AC XY: 3AN XY: 34389
GnomAD3 exomes AF: 0.0000440 AC: 8AN: 181767Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66421
GnomAD4 exome AF: 0.0000128 AC: 14AN: 1096985Hom.: 0 Cov.: 30 AF XY: 0.00000276 AC XY: 1AN XY: 362413
GnomAD4 genome AF: 0.000107 AC: 12AN: 112225Hom.: 0 Cov.: 23 AF XY: 0.0000872 AC XY: 3AN XY: 34389
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at