rs1799724
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 0.0879 in 151822 control chromosomes in the gnomAD Genomes database, including 835 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).
Frequency
Genomes: 𝑓 0.088 ( 835 hom., cov: 31)
Consequence
Unknown
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.39
Links
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.166 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: 0.0879 AC: 13352AN: 151822Hom.: 835 Cov.: 31
GnomAD3 genomes
AF:
AC:
13352
AN:
151822
Hom.:
Cov.:
31
Gnomad AFR
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Bravo
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Asia WGS
AF:
AC:
404
AN:
3478
ClinVar
Significance: risk factor
Submissions summary: Other:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Alzheimer disease, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Jul 01, 2005 | - - |
Vascular dementia, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Jul 01, 2005 | - - |
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