chr9-96819322-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001001662.3(ZNF782):āc.701A>Gā(p.Asn234Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000771 in 1,608,782 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001001662.3 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 |
---|---|---|---|---|---|---|---|
ZNF782 | NM_001001662.3 | c.701A>G | p.Asn234Ser | missense_variant | 6/6 | ENST00000481138.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF782 | ENST00000481138.6 | c.701A>G | p.Asn234Ser | missense_variant | 6/6 | 1 | NM_001001662.3 | P1 | |
ZNF782 | ENST00000535338.5 | c.701A>G | p.Asn234Ser | missense_variant | 5/5 | 3 | P1 | ||
ZNF782 | ENST00000289032.12 | n.666A>G | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000453 AC: 69AN: 152240Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000212 AC: 52AN: 244976Hom.: 0 AF XY: 0.000211 AC XY: 28AN XY: 132598
GnomAD4 exome AF: 0.0000378 AC: 55AN: 1456542Hom.: 0 Cov.: 33 AF XY: 0.0000428 AC XY: 31AN XY: 724394
GnomAD4 genome AF: 0.000453 AC: 69AN: 152240Hom.: 1 Cov.: 33 AF XY: 0.000686 AC XY: 51AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 11, 2022 | The c.701A>G (p.N234S) alteration is located in exon 6 (coding exon 4) of the ZNF782 gene. This alteration results from a A to G substitution at nucleotide position 701, causing the asparagine (N) at amino acid position 234 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at