chr19-37362841-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001353803.2(ZNF875):c.989G>A(p.Arg330Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000725 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001353803.2 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 |
---|---|---|---|---|---|---|---|
ZNF875 | NM_001353803.2 | c.989G>A | p.Arg330Gln | missense_variant | 5/5 | ENST00000392153.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF875 | ENST00000392153.8 | c.989G>A | p.Arg330Gln | missense_variant | 5/5 | 1 | NM_001353803.2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152088Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000875 AC: 22AN: 251446Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135886
GnomAD4 exome AF: 0.0000725 AC: 106AN: 1461882Hom.: 0 Cov.: 32 AF XY: 0.0000701 AC XY: 51AN XY: 727246
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152088Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74288
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 19, 2023 | The c.1046G>A (p.R349Q) alteration is located in exon 6 (coding exon 4) of the HKR1 gene. This alteration results from a G to A substitution at nucleotide position 1046, causing the arginine (R) at amino acid position 349 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