chr19-58084810-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001145543.2(ZSCAN18):c.1408G>A(p.Ala470Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000697 in 1,435,126 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A470E) has been classified as Uncertain significance.
Frequency
Consequence
NM_001145543.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZSCAN18 | NM_001145543.2 | c.1408G>A | p.Ala470Thr | missense_variant | Exon 7 of 7 | ENST00000601144.6 | NP_001139015.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.97e-7 AC: 1AN: 1435126Hom.: 0 Cov.: 31 AF XY: 0.00000140 AC XY: 1AN XY: 712598
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1576G>A (p.A526T) alteration is located in exon 7 (coding exon 7) of the ZSCAN18 gene. This alteration results from a G to A substitution at nucleotide position 1576, causing the alanine (A) at amino acid position 526 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