19-12145506-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.910G>A(p.Glu304Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000263 in 151,936 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 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.910G>A | p.Glu304Lys | missense_variant | Exon 4 of 4 | ENST00000439556.3 | NP_660276.2 | |
ZNF625 | NR_037801.2 | n.1082G>A | non_coding_transcript_exon_variant | Exon 4 of 4 | ||||
ZNF625-ZNF20 | NR_037802.1 | n.364+1889G>A | intron_variant | Intron 3 of 7 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151936Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.89e-7 AC: 1AN: 1452238Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 722510
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151936Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74198
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.910G>A (p.E304K) 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 910, causing the glutamic acid (E) at amino acid position 304 to be replaced by a lysine (K). 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