7-149104193-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001001661.3(ZNF425):c.1678G>T(p.Asp560Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000676 in 1,612,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001001661.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF425 | NM_001001661.3 | c.1678G>T | p.Asp560Tyr | missense_variant | Exon 4 of 4 | ENST00000378061.7 | NP_001001661.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152160Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000360 AC: 9AN: 249880Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135252
GnomAD4 exome AF: 0.0000705 AC: 103AN: 1460582Hom.: 0 Cov.: 88 AF XY: 0.0000633 AC XY: 46AN XY: 726430
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152160Hom.: 0 Cov.: 34 AF XY: 0.0000404 AC XY: 3AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1678G>T (p.D560Y) alteration is located in exon 4 (coding exon 4) of the ZNF425 gene. This alteration results from a G to T substitution at nucleotide position 1678, causing the aspartic acid (D) at amino acid position 560 to be replaced by a tyrosine (Y). 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