chr10-43557638-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001099282.2(ZNF239):c.442G>A(p.Asp148Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000936 in 1,614,092 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_001099282.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF239 | NM_001099282.2 | c.442G>A | p.Asp148Asn | missense_variant | 4/4 | ENST00000374446.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF239 | ENST00000374446.7 | c.442G>A | p.Asp148Asn | missense_variant | 4/4 | 1 | NM_001099282.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152250Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000441 AC: 11AN: 249298Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135256
GnomAD4 exome AF: 0.0000937 AC: 137AN: 1461842Hom.: 0 Cov.: 42 AF XY: 0.0000908 AC XY: 66AN XY: 727220
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 27, 2023 | The c.442G>A (p.D148N) alteration is located in exon 2 (coding exon 1) of the ZNF239 gene. This alteration results from a G to A substitution at nucleotide position 442, causing the aspartic acid (D) at amino acid position 148 to be replaced by an asparagine (N). 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