19-12349939-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_030824.3(ZNF442):c.1646G>T(p.Cys549Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000694 in 1,614,054 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030824.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF442 | ENST00000242804.9 | c.1646G>T | p.Cys549Phe | missense_variant | Exon 6 of 6 | 2 | NM_030824.3 | ENSP00000242804.4 | ||
ZNF442 | ENST00000545749.2 | c.1646G>T | p.Cys549Phe | missense_variant | Exon 4 of 4 | 5 | ENSP00000440162.2 | |||
ZNF442 | ENST00000438182.5 | c.1439G>T | p.Cys480Phe | missense_variant | Exon 3 of 3 | 2 | ENSP00000388634.1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152232Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251396Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135872
GnomAD4 exome AF: 0.0000732 AC: 107AN: 1461822Hom.: 0 Cov.: 31 AF XY: 0.0000646 AC XY: 47AN XY: 727206
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1646G>T (p.C549F) alteration is located in exon 6 (coding exon 4) of the ZNF442 gene. This alteration results from a G to T substitution at nucleotide position 1646, causing the cysteine (C) at amino acid position 549 to be replaced by a phenylalanine (F). 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