rs12935091
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000564225.5(ZNF19):c.-190+3649T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0297 in 152,294 control chromosomes in the GnomAD database, including 91 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 0.030 ( 91 hom., cov: 32)
Consequence
ZNF19
ENST00000564225.5 intron
ENST00000564225.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0170
Genes affected
ZNF19 (HGNC:12981): (zinc finger protein 19) The protein encoded by this gene contains a zinc finger, a nucleic acid-binding domain present in many transcription factors. This gene is located in a region next to ZNF23, a gene also encoding a zinc finger protein, on chromosome 16. [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=-0.9).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0297 (4529/152294) while in subpopulation NFE AF= 0.0474 (3223/68016). AF 95% confidence interval is 0.046. There are 91 homozygotes in gnomad4. There are 2104 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 91 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF19 | ENST00000564225.5 | c.-190+3649T>C | intron_variant | 2 | |||||
ZNF19 | ENST00000566202.5 | c.-189-6557T>C | intron_variant | 5 | |||||
ZNF19 | ENST00000568446.1 | n.324+3649T>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0298 AC: 4530AN: 152176Hom.: 91 Cov.: 32
GnomAD3 genomes
?
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4530
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152176
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0297 AC: 4529AN: 152294Hom.: 91 Cov.: 32 AF XY: 0.0283 AC XY: 2104AN XY: 74458
GnomAD4 genome
?
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4529
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152294
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32
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2104
AN XY:
74458
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19
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at