rs40457
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 0.574 in 152,024 control chromosomes in the GnomAD database, including 26,242 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain risk allele (no stars).
Frequency
Genomes: 𝑓 0.57 ( 26242 hom., cov: 31)
Consequence
Unknown
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.97
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes AF: 0.573 AC: 87110AN: 151904Hom.: 26214 Cov.: 31
GnomAD3 genomes
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87110
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151904
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.574 AC: 87195AN: 152024Hom.: 26242 Cov.: 31 AF XY: 0.569 AC XY: 42287AN XY: 74286
GnomAD4 genome
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87195
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152024
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Cov.:
31
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AC XY:
42287
AN XY:
74286
Gnomad4 AFR
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Asia WGS
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1227
AN:
3478
ClinVar
Significance: Uncertain risk allele
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Leprosy, susceptibility to, 1 Other:1
Uncertain risk allele, no assertion criteria provided | case-control | Centro Dermatológico Federico Lleras Acosta, Hospital Universitario Centro Dermatológico Federico Lleras Acosta | Jun 10, 2022 | - - |
Computational 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