19-12145460-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145233.4(ZNF625):c.956G>A(p.Arg319Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,461,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145233.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF625 | NM_145233.4 | c.956G>A | p.Arg319Gln | missense_variant | Exon 4 of 4 | ENST00000439556.3 | NP_660276.2 | |
ZNF625 | NR_037801.2 | n.1128G>A | non_coding_transcript_exon_variant | Exon 4 of 4 | ||||
ZNF625-ZNF20 | NR_037802.1 | n.364+1935G>A | intron_variant | Intron 3 of 7 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251444Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135892
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461882Hom.: 0 Cov.: 29 AF XY: 0.0000151 AC XY: 11AN XY: 727236
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.956G>A (p.R319Q) alteration is located in exon 4 (coding exon 4) of the ZNF625 gene. This alteration results from a G to A substitution at nucleotide position 956, causing the arginine (R) at amino acid position 319 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