19-12145311-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.1105G>A(p.Glu369Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,607,084 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E369Q) has been classified 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.1105G>A | p.Glu369Lys | missense_variant | Exon 4 of 4 | ENST00000439556.3 | NP_660276.2 | |
ZNF625 | NR_037801.2 | n.1277G>A | non_coding_transcript_exon_variant | Exon 4 of 4 | ||||
ZNF625-ZNF20 | NR_037802.1 | n.364+2084G>A | intron_variant | Intron 3 of 7 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 247156Hom.: 0 AF XY: 0.0000300 AC XY: 4AN XY: 133528
GnomAD4 exome AF: 0.0000131 AC: 19AN: 1454750Hom.: 0 Cov.: 29 AF XY: 0.0000111 AC XY: 8AN XY: 722878
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152334Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1105G>A (p.E369K) 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 1105, causing the glutamic acid (E) at amino acid position 369 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