17-76082607-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_180990.4(ZACN):āc.1193C>Gā(p.Ala398Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,090 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_180990.4 missense
Scores
Clinical Significance
Conservation
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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.1193C>G | p.Ala398Gly | missense_variant | Exon 9 of 9 | 1 | NM_180990.4 | ENSP00000334854.5 | ||
EXOC7 | ENST00000589210 | c.*1041G>C | 3_prime_UTR_variant | Exon 19 of 19 | 1 | NM_001013839.4 | ENSP00000468404.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248866Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134836
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461090Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726874
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1193C>G (p.A398G) alteration is located in exon 9 (coding exon 9) of the ZACN gene. This alteration results from a C to G substitution at nucleotide position 1193, causing the alanine (A) at amino acid position 398 to be replaced by a glycine (G). 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