7-64978261-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The ENST00000282869.11(ZNF117):c.1310G>T(p.Arg437Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000025 in 1,440,438 control chromosomes in the GnomAD database, with no homozygous occurrence. 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
ENST00000282869.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF117 | NM_015852.5 | c.1310G>T | p.Arg437Ile | missense_variant | 4/4 | ENST00000282869.11 | NP_056936.2 | |
ERV3-1-ZNF117 | NM_001348050.2 | c.1310G>T | p.Arg437Ile | missense_variant | 4/4 | NP_001334979.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF117 | ENST00000282869.11 | c.1310G>T | p.Arg437Ile | missense_variant | 4/4 | 1 | NM_015852.5 | ENSP00000282869 | P1 | |
ZNF117 | ENST00000620222.4 | c.1310G>T | p.Arg437Ile | missense_variant | 3/3 | 1 | ENSP00000479944 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 10AN: 145086Hom.: 0 Cov.: 34 FAILED QC
GnomAD3 exomes AF: 0.00000808 AC: 2AN: 247618Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134390
GnomAD4 exome AF: 0.0000250 AC: 36AN: 1440438Hom.: 0 Cov.: 33 AF XY: 0.0000307 AC XY: 22AN XY: 716356
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000689 AC: 10AN: 145218Hom.: 0 Cov.: 34 AF XY: 0.0000987 AC XY: 7AN XY: 70922
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2024 | 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