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GeneBe

rs1024611

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP5BP4BA1

The variant allele was found at a frequency of 0.287 in 152044 control chromosomes in the gnomAD Genomes database, including 6908 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic,risk factor (no stars).

Frequency

Genomes: 𝑓 0.29 ( 6908 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Pathogenic; risk factor no assertion criteria provided P:1O:3

Conservation

PhyloP100: -0.103

Links

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ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

PP5
?
Variant 17-34252769-A-G is Pathogenic according to our data. Variant chr17-34252769-A-G is described in ClinVar as [Pathogenic, risk_factor]. Clinvar id is 14207.Status of the report is no_assertion_criteria_provided, 0 stars.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).. Strength limited to SUPPORTING due to the PP5.
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 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:
0.287
AC:
43582
AN:
152044
Hom.:
6908
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.201
Gnomad AMI
AF:
0.140
Gnomad AMR
AF:
0.431
Gnomad ASJ
AF:
0.282
Gnomad EAS
AF:
0.556
Gnomad SAS
AF:
0.343
Gnomad FIN
AF:
0.344
Gnomad MID
AF:
0.326
Gnomad NFE
AF:
0.275
Gnomad OTH
AF:
0.284
Alfa
AF:
0.268
Hom.:
529
Bravo
AF:
0.290
Asia WGS
AF:
0.439
AC:
1527
AN:
3478

ClinVar

Significance: Pathogenic; risk factor
Submissions summary: Pathogenic:1Other:3
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Coronary artery disease, development of, in HIV Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMJan 15, 2009- -
Mycobacterium tuberculosis, susceptibility to Other:1
risk factor, no assertion criteria providedliterature onlyOMIMJan 15, 2009- -
Coronary artery disease, modifier of Other:1
risk factor, no assertion criteria providedliterature onlyOMIMJan 15, 2009- -
Spina bifida, susceptibility to Other:1
risk factor, no assertion criteria providedliterature onlyOMIMJan 15, 2009- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
2.4
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: rs1024611; hg19: chr17-32579788; API