7-149848271-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001099220.3(ZNF862):c.778A>T(p.Ser260Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0003 in 1,612,104 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001099220.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF862 | NM_001099220.3 | c.778A>T | p.Ser260Cys | missense_variant | 4/8 | ENST00000223210.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF862 | ENST00000223210.5 | c.778A>T | p.Ser260Cys | missense_variant | 4/8 | 5 | NM_001099220.3 | P1 | |
ZNF862 | ENST00000488265.1 | n.145A>T | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000111 AC: 27AN: 243850Hom.: 0 AF XY: 0.0000830 AC XY: 11AN XY: 132532
GnomAD4 exome AF: 0.000315 AC: 460AN: 1459870Hom.: 0 Cov.: 32 AF XY: 0.000310 AC XY: 225AN XY: 726016
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2022 | The c.778A>T (p.S260C) alteration is located in exon 4 (coding exon 4) of the ZNF862 gene. This alteration results from a A to T substitution at nucleotide position 778, causing the serine (S) at amino acid position 260 to be replaced by a cysteine (C). 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