17-76081647-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_180990.4(ZACN):c.772G>A(p.Ala258Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,232 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
Frequency
Consequence
NM_180990.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZACN | ENST00000334586.10 | c.772G>A | p.Ala258Thr | missense_variant | Exon 7 of 9 | 1 | NM_180990.4 | ENSP00000334854.5 | ||
EXOC7 | ENST00000589210 | c.*2001C>T | 3_prime_UTR_variant | Exon 19 of 19 | 1 | NM_001013839.4 | ENSP00000468404.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251208Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135796
GnomAD4 exome Cov.: 34
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.772G>A (p.A258T) alteration is located in exon 7 (coding exon 7) of the ZACN gene. This alteration results from a G to A substitution at nucleotide position 772, causing the alanine (A) at amino acid position 258 to be replaced by a threonine (T). 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