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GeneBe

rs405509

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 0.576 in 152,040 control chromosomes in the GnomAD database, including 26,172 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (no stars).

Frequency

Genomes: 𝑓 0.58 ( 26172 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

drug response no assertion criteria provided O:1

Conservation

PhyloP100: 0.310
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 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:
0.575
AC:
87415
AN:
151922
Hom.:
26137
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.747
Gnomad AMI
AF:
0.562
Gnomad AMR
AF:
0.503
Gnomad ASJ
AF:
0.535
Gnomad EAS
AF:
0.305
Gnomad SAS
AF:
0.443
Gnomad FIN
AF:
0.557
Gnomad MID
AF:
0.497
Gnomad NFE
AF:
0.523
Gnomad OTH
AF:
0.577
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.576
AC:
87504
AN:
152040
Hom.:
26172
Cov.:
31
AF XY:
0.572
AC XY:
42525
AN XY:
74316
show subpopulations
Gnomad4 AFR
AF:
0.747
Gnomad4 AMR
AF:
0.502
Gnomad4 ASJ
AF:
0.535
Gnomad4 EAS
AF:
0.306
Gnomad4 SAS
AF:
0.444
Gnomad4 FIN
AF:
0.557
Gnomad4 NFE
AF:
0.523
Gnomad4 OTH
AF:
0.576
Alfa
AF:
0.534
Hom.:
32258
Bravo
AF:
0.577
Asia WGS
AF:
0.428
AC:
1492
AN:
3478

ClinVar

Significance: drug response
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Warfarin response Other:1
drug response, no assertion criteria providedresearchPharmacogenomics Lab, Chungbuk National UniversityAug 31, 2010- likely responsive

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
Cadd
Benign
10
Dann
Benign
0.77

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: rs405509; hg19: chr19-45408836; API