19-57572750-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017879.3(ZNF416):c.1154G>A(p.Gly385Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000793 in 1,614,054 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_017879.3 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 |
---|---|---|---|---|---|---|---|---|
ZNF416 | NM_017879.3 | c.1154G>A | p.Gly385Asp | missense_variant | Exon 4 of 4 | ENST00000196489.4 | NP_060349.1 | |
ZNF416 | NM_001353405.2 | c.938G>A | p.Gly313Asp | missense_variant | Exon 3 of 3 | NP_001340334.1 | ||
ZNF416 | XM_024451594.2 | c.1094G>A | p.Gly365Asp | missense_variant | Exon 5 of 5 | XP_024307362.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000143 AC: 36AN: 251458Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135898
GnomAD4 exome AF: 0.0000828 AC: 121AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.0000976 AC XY: 71AN XY: 727246
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1154G>A (p.G385D) alteration is located in exon 4 (coding exon 4) of the ZNF416 gene. This alteration results from a G to A substitution at nucleotide position 1154, causing the glycine (G) at amino acid position 385 to be replaced by an aspartic acid (D). 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