19-58469800-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014347.3(ZNF324):c.194C>T(p.Thr65Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000737 in 1,600,864 control chromosomes in the GnomAD database, including 1 homozygotes. 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_014347.3 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 |
---|---|---|---|---|---|---|---|---|
ZNF324 | NM_014347.3 | c.194C>T | p.Thr65Met | missense_variant | Exon 3 of 4 | ENST00000196482.4 | NP_055162.1 | |
ZNF324 | XM_005258713.5 | c.209C>T | p.Thr70Met | missense_variant | Exon 3 of 4 | XP_005258770.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000659 AC: 15AN: 227498Hom.: 0 AF XY: 0.0000653 AC XY: 8AN XY: 122586
GnomAD4 exome AF: 0.0000752 AC: 109AN: 1448648Hom.: 1 Cov.: 31 AF XY: 0.0000779 AC XY: 56AN XY: 719154
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.194C>T (p.T65M) alteration is located in exon 3 (coding exon 2) of the ZNF324 gene. This alteration results from a C to T substitution at nucleotide position 194, causing the threonine (T) at amino acid position 65 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