rs2230660
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001099282.2(ZNF239):c.515C>T(p.Ala172Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,613,930 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A172G) has been classified as Likely benign.
Frequency
Consequence
NM_001099282.2 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF239 | NM_001099282.2 | c.515C>T | p.Ala172Val | missense_variant | 4/4 | ENST00000374446.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF239 | ENST00000374446.7 | c.515C>T | p.Ala172Val | missense_variant | 4/4 | 1 | NM_001099282.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152026Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000442 AC: 11AN: 249110Hom.: 0 AF XY: 0.0000666 AC XY: 9AN XY: 135162
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461786Hom.: 0 Cov.: 65 AF XY: 0.0000248 AC XY: 18AN XY: 727202
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152144Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74374
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at