chr15-90360423-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001004309.3(ZNF774):c.592C>T(p.Arg198Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,684 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R198G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001004309.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF774 | ENST00000354377.8 | c.592C>T | p.Arg198Cys | missense_variant | Exon 4 of 4 | 1 | NM_001004309.3 | ENSP00000346348.3 | ||
ZNF774 | ENST00000379090.9 | c.211+1466C>T | intron_variant | Intron 3 of 4 | 1 | ENSP00000368383.5 | ||||
ZNF774 | ENST00000558115.1 | n.584C>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 3 | |||||
ZNF774 | ENST00000560038.5 | n.*523C>T | downstream_gene_variant | 4 | ENSP00000453202.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152072Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250996Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135702
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461612Hom.: 0 Cov.: 33 AF XY: 0.0000151 AC XY: 11AN XY: 727130
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152072Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.592C>T (p.R198C) alteration is located in exon 4 (coding exon 3) of the ZNF774 gene. This alteration results from a C to T substitution at nucleotide position 592, causing the arginine (R) at amino acid position 198 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