16-57997893-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_020807.3(ZNF319):c.373G>A(p.Val125Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000787 in 1,613,552 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 (★).
Frequency
Consequence
NM_020807.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF319 | NM_020807.3 | c.373G>A | p.Val125Met | missense_variant | Exon 2 of 2 | ENST00000299237.3 | NP_065858.1 | |
ZNF319 | NM_001384365.1 | c.373G>A | p.Val125Met | missense_variant | Exon 2 of 2 | NP_001371294.1 | ||
ZNF319 | NM_001384366.1 | c.373G>A | p.Val125Met | missense_variant | Exon 3 of 3 | NP_001371295.1 | ||
ZNF319 | NM_001384367.1 | c.373G>A | p.Val125Met | missense_variant | Exon 3 of 3 | NP_001371296.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152268Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000797 AC: 20AN: 250872Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135766
GnomAD4 exome AF: 0.0000753 AC: 110AN: 1461166Hom.: 0 Cov.: 33 AF XY: 0.0000688 AC XY: 50AN XY: 726898
GnomAD4 genome AF: 0.000112 AC: 17AN: 152386Hom.: 0 Cov.: 34 AF XY: 0.0000805 AC XY: 6AN XY: 74520
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.373G>A (p.V125M) alteration is located in exon 2 (coding exon 1) of the ZNF319 gene. This alteration results from a G to A substitution at nucleotide position 373, causing the valine (V) at amino acid position 125 to be replaced by a methionine (M). 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