rs12612930
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000410075.5(ZNF638):c.-203+21901T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0525 in 152,276 control chromosomes in the GnomAD database, including 976 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.
Frequency
Genomes: 𝑓 0.053 ( 976 hom., cov: 32)
Consequence
ZNF638
ENST00000410075.5 intron
ENST00000410075.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0290
Genes affected
ZNF638 (HGNC:17894): (zinc finger protein 638) The protein encoded by this gene is a nucleoplasmic protein. It binds cytidine-rich sequences in double-stranded DNA. This protein has three types of domains: MH1, MH2 (repeated three times) and MH3. It is associated with packaging, transferring, or processing transcripts. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
use as main transcript | n.71298655T>C | intergenic_region |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF638 | ENST00000410075.5 | c.-203+21901T>C | intron_variant | 1 | ENSP00000485608.2 | |||||
ZNF638 | ENST00000466330.5 | c.-85+21901T>C | intron_variant | 3 | ENSP00000485494.1 | |||||
ZNF638 | ENST00000466975.5 | c.116+21901T>C | intron_variant | 4 | ENSP00000485154.2 | |||||
ZNF638 | ENST00000494621.5 | c.-217+21901T>C | intron_variant | 3 | ENSP00000485618.2 |
Frequencies
GnomAD3 genomes AF: 0.0525 AC: 7991AN: 152158Hom.: 977 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0525 AC: 8001AN: 152276Hom.: 976 Cov.: 32 AF XY: 0.0590 AC XY: 4391AN XY: 74472
GnomAD4 genome
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996
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at