19-53408759-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001040185.3(ZNF765):c.1204C>T(p.Arg402Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000676 in 1,613,010 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001040185.3 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 |
---|---|---|---|---|---|---|---|
ZNF765 | NM_001040185.3 | c.1204C>T | p.Arg402Cys | missense_variant | 4/4 | ENST00000396408.8 | |
ZNF765-ZNF761 | NM_001350496.2 | c.-1345+6568C>T | intron_variant | ||||
ZNF765 | NM_001350495.2 | c.1045C>T | p.Arg349Cys | missense_variant | 3/3 | ||
ZNF765 | NR_146721.2 | n.260+6568C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF765 | ENST00000396408.8 | c.1204C>T | p.Arg402Cys | missense_variant | 4/4 | 1 | NM_001040185.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000990 AC: 15AN: 151578Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000836 AC: 21AN: 251246Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135852
GnomAD4 exome AF: 0.0000643 AC: 94AN: 1461432Hom.: 0 Cov.: 83 AF XY: 0.0000770 AC XY: 56AN XY: 727026
GnomAD4 genome ? AF: 0.0000990 AC: 15AN: 151578Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 73998
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2023 | The c.1204C>T (p.R402C) alteration is located in exon 4 (coding exon 3) of the ZNF765 gene. This alteration results from a C to T substitution at nucleotide position 1204, causing the arginine (R) at amino acid position 402 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