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GeneBe

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

risk factor no assertion criteria provided O:2

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

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0879
AC:
13352
AN:
151822
Hom.:
835
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0309
Gnomad AMI
AF:
0.0826
Gnomad AMR
AF:
0.172
Gnomad ASJ
AF:
0.255
Gnomad EAS
AF:
0.132
Gnomad SAS
AF:
0.123
Gnomad FIN
AF:
0.0557
Gnomad MID
AF:
0.142
Gnomad NFE
AF:
0.0939
Gnomad OTH
AF:
0.0986
Alfa
AF:
0.121
Hom.:
1422
Bravo
AF:
0.0935
Asia WGS
AF:
0.116
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 providedliterature onlyOMIMJul 01, 2005- -
Vascular dementia, susceptibility to Other:1
risk factor, no assertion criteria providedliterature onlyOMIMJul 01, 2005- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
0.33
Dann
Benign
0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1799724; hg19: chr6-31542482;