chr10-47368499-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_153034.4(ZNF488):c.331C>T(p.Arg111Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,613,796 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 6/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R111G) has been classified as Uncertain significance.
Frequency
Consequence
NM_153034.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF488 | NM_153034.4 | c.331C>T | p.Arg111Trp | missense_variant | 2/2 | ENST00000585316.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF488 | ENST00000585316.3 | c.331C>T | p.Arg111Trp | missense_variant | 2/2 | 1 | NM_153034.4 | A2 | |
ZNF488 | ENST00000591025.1 | c.10C>T | p.Arg4Trp | missense_variant | 3/3 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000885 AC: 22AN: 248684Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 134830
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461496Hom.: 1 Cov.: 31 AF XY: 0.0000715 AC XY: 52AN XY: 727066
GnomAD4 genome ? AF: 0.0000919 AC: 14AN: 152300Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74456
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2022 | 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