chr19-53408592-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.1037G>A(p.Arg346His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,613,568 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 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.1037G>A | p.Arg346His | missense_variant | 4/4 | ENST00000396408.8 | |
ZNF765-ZNF761 | NM_001350496.2 | c.-1345+6401G>A | intron_variant | ||||
ZNF765 | NM_001350495.2 | c.878G>A | p.Arg293His | missense_variant | 3/3 | ||
ZNF765 | NR_146721.2 | n.260+6401G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF765 | ENST00000396408.8 | c.1037G>A | p.Arg346His | missense_variant | 4/4 | 1 | NM_001040185.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151882Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251252Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135858
GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461568Hom.: 0 Cov.: 87 AF XY: 0.0000344 AC XY: 25AN XY: 727086
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152000Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | The c.1037G>A (p.R346H) 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 1037, causing the arginine (R) at amino acid position 346 to be replaced by a histidine (H). 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