rs12576211
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The variant allele was found at a frequency of 0.268 in 152,020 control chromosomes in the GnomAD database, including 6,518 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 0.27 ( 6518 hom., cov: 32)
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.23
Genes affected
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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=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
use as main transcript | n.125116097G>A | intergenic_region |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KRT18P59 | ENST00000534728.1 | n.1785+1152G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.267 AC: 40618AN: 151902Hom.: 6503 Cov.: 32
GnomAD3 genomes
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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: 0.268 AC: 40668AN: 152020Hom.: 6518 Cov.: 32 AF XY: 0.261 AC XY: 19395AN XY: 74314
GnomAD4 genome
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40668
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152020
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32
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19395
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74314
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Asia WGS
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672
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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