19-19711656-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021030.3(ZNF14):c.1625G>A(p.Arg542His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,613,622 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_021030.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000396 AC: 6AN: 151648Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000916 AC: 23AN: 251218Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135766
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461854Hom.: 0 Cov.: 32 AF XY: 0.0000289 AC XY: 21AN XY: 727222
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151768Hom.: 0 Cov.: 33 AF XY: 0.0000539 AC XY: 4AN XY: 74200
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1625G>A (p.R542H) alteration is located in exon 4 (coding exon 4) of the ZNF14 gene. This alteration results from a G to A substitution at nucleotide position 1625, causing the arginine (R) at amino acid position 542 to be replaced by a histidine (H). 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