chrX-47914996-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_007137.5(ZNF81):c.350G>T(p.Gly117Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00215 in 1,204,611 control chromosomes in the GnomAD database, including 36 homozygotes. There are 677 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G117D) has been classified as Uncertain significance.
Frequency
Consequence
NM_007137.5 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF81 | NM_007137.5 | c.350G>T | p.Gly117Val | missense_variant | 5/5 | ENST00000338637.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF81 | ENST00000338637.13 | c.350G>T | p.Gly117Val | missense_variant | 5/5 | 3 | NM_007137.5 | P1 | |
ZNF81 | ENST00000376954.6 | c.350G>T | p.Gly117Val | missense_variant | 6/6 | 5 | P1 | ||
ZNF81 | ENST00000376950.4 | c.277+19056G>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0109 AC: 1215AN: 111311Hom.: 19 Cov.: 23 AF XY: 0.00928 AC XY: 311AN XY: 33501
GnomAD3 exomes AF: 0.00306 AC: 536AN: 174889Hom.: 8 AF XY: 0.00197 AC XY: 121AN XY: 61521
GnomAD4 exome AF: 0.00125 AC: 1367AN: 1093250Hom.: 17 Cov.: 30 AF XY: 0.00100 AC XY: 359AN XY: 359108
GnomAD4 genome AF: 0.0110 AC: 1224AN: 111361Hom.: 19 Cov.: 23 AF XY: 0.00948 AC XY: 318AN XY: 33561
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 06, 2016 | This alteration is classified as 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