chr10-43557455-A-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001099282.2(ZNF239):c.625T>G(p.Cys209Gly) variant causes a missense change. The variant allele was found at a frequency of 0.54 in 1,613,868 control chromosomes in the GnomAD database, including 236,367 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001099282.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF239 | NM_001099282.2 | c.625T>G | p.Cys209Gly | missense_variant | 4/4 | ENST00000374446.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF239 | ENST00000374446.7 | c.625T>G | p.Cys209Gly | missense_variant | 4/4 | 1 | NM_001099282.2 | P1 | |
ZNF239 | ENST00000306006.10 | c.625T>G | p.Cys209Gly | missense_variant | 2/2 | 1 | P1 | ||
ZNF239 | ENST00000426961.1 | c.625T>G | p.Cys209Gly | missense_variant | 3/3 | 2 | P1 | ||
ZNF239 | ENST00000535642.5 | c.625T>G | p.Cys209Gly | missense_variant | 2/2 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.536 AC: 81449AN: 151984Hom.: 22106 Cov.: 33
GnomAD3 exomes AF: 0.552 AC: 137828AN: 249516Hom.: 38270 AF XY: 0.557 AC XY: 75339AN XY: 135358
GnomAD4 exome AF: 0.540 AC: 789849AN: 1461766Hom.: 214242 Cov.: 67 AF XY: 0.542 AC XY: 394496AN XY: 727194
GnomAD4 genome ? AF: 0.536 AC: 81520AN: 152102Hom.: 22125 Cov.: 33 AF XY: 0.541 AC XY: 40200AN XY: 74374
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at