17-76082027-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_180990.4(ZACN):c.1026C>A(p.Asn342Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000892 in 1,458,110 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZACN | ENST00000334586.10 | c.1026C>A | p.Asn342Lys | missense_variant | Exon 8 of 9 | 1 | NM_180990.4 | ENSP00000334854.5 | ||
EXOC7 | ENST00000589210 | c.*1621G>T | 3_prime_UTR_variant | Exon 19 of 19 | 1 | NM_001013839.4 | ENSP00000468404.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000420 AC: 1AN: 238162Hom.: 0 AF XY: 0.00000767 AC XY: 1AN XY: 130396
GnomAD4 exome AF: 0.00000892 AC: 13AN: 1458110Hom.: 0 Cov.: 33 AF XY: 0.00000827 AC XY: 6AN XY: 725330
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1026C>A (p.N342K) alteration is located in exon 8 (coding exon 8) of the ZACN gene. This alteration results from a C to A substitution at nucleotide position 1026, causing the asparagine (N) at amino acid position 342 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