19-53408423-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.868C>T(p.Arg290Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000226 in 1,613,920 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R290H) has been classified 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.868C>T | p.Arg290Cys | missense_variant | 4/4 | ENST00000396408.8 | |
ZNF765-ZNF761 | NM_001350496.2 | c.-1345+6232C>T | intron_variant | ||||
ZNF765 | NM_001350495.2 | c.709C>T | p.Arg237Cys | missense_variant | 3/3 | ||
ZNF765 | NR_146721.2 | n.260+6232C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF765 | ENST00000396408.8 | c.868C>T | p.Arg290Cys | missense_variant | 4/4 | 1 | NM_001040185.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000362 AC: 55AN: 151992Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000231 AC: 58AN: 251224Hom.: 0 AF XY: 0.000213 AC XY: 29AN XY: 135870
GnomAD4 exome AF: 0.000211 AC: 309AN: 1461810Hom.: 0 Cov.: 86 AF XY: 0.000182 AC XY: 132AN XY: 727196
GnomAD4 genome ? AF: 0.000368 AC: 56AN: 152110Hom.: 0 Cov.: 33 AF XY: 0.000363 AC XY: 27AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 12, 2023 | The c.868C>T (p.R290C) 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 868, causing the arginine (R) at amino acid position 290 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