chr19-53407929-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001040185.3(ZNF765):c.374G>A(p.Arg125Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000678 in 1,614,124 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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.374G>A | p.Arg125Gln | missense_variant | 4/4 | ENST00000396408.8 | |
ZNF765-ZNF761 | NM_001350496.2 | c.-1345+5738G>A | intron_variant | ||||
ZNF765 | NM_001350495.2 | c.215G>A | p.Arg72Gln | missense_variant | 3/3 | ||
ZNF765 | NR_146721.2 | n.260+5738G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF765 | ENST00000396408.8 | c.374G>A | p.Arg125Gln | missense_variant | 4/4 | 1 | NM_001040185.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000394 AC: 60AN: 152162Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000518 AC: 130AN: 250890Hom.: 0 AF XY: 0.000523 AC XY: 71AN XY: 135792
GnomAD4 exome AF: 0.000707 AC: 1034AN: 1461844Hom.: 1 Cov.: 31 AF XY: 0.000715 AC XY: 520AN XY: 727220
GnomAD4 genome AF: 0.000394 AC: 60AN: 152280Hom.: 0 Cov.: 33 AF XY: 0.000282 AC XY: 21AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2022 | The c.374G>A (p.R125Q) alteration is located in exon 4 (coding exon 3) of the ZNF765 gene. This alteration results from a G to A substitution at nucleotide position 374, causing the arginine (R) at amino acid position 125 to be replaced by a glutamine (Q). 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