19-52501862-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001099694.2(ZNF578):c.17C>T(p.Ala6Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000276 in 1,613,566 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001099694.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000355 AC: 54AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000359 AC: 90AN: 250654Hom.: 0 AF XY: 0.000347 AC XY: 47AN XY: 135554
GnomAD4 exome AF: 0.000267 AC: 390AN: 1461306Hom.: 5 Cov.: 31 AF XY: 0.000282 AC XY: 205AN XY: 727026
GnomAD4 genome AF: 0.000361 AC: 55AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.000510 AC XY: 38AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.17C>T (p.A6V) alteration is located in exon 4 (coding exon 1) of the ZNF578 gene. This alteration results from a C to T substitution at nucleotide position 17, causing the alanine (A) at amino acid position 6 to be replaced by a valine (V). 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