7-76424977-T-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001110354.2(ZP3):āc.13T>Gā(p.Tyr5Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000733 in 1,542,380 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001110354.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000560 AC: 83AN: 148170Hom.: 1 AF XY: 0.000389 AC XY: 31AN XY: 79750
GnomAD4 exome AF: 0.0000719 AC: 100AN: 1390246Hom.: 1 Cov.: 30 AF XY: 0.0000583 AC XY: 40AN XY: 685552
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.13T>G (p.Y5D) alteration is located in exon 1 (coding exon 1) of the ZP3 gene. This alteration results from a T to G substitution at nucleotide position 13, causing the tyrosine (Y) at amino acid position 5 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
ZP3-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at