rs405509

chr19-44905579-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: drug response no assertion criteria provided O:1
• Conservation: PhyloP100: 0.310

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

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

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

Submissions by phenotype

Warfarin response Other:1

drug response, no assertion criteria provided

research

Pharmacogenomics Lab, Chungbuk National University

Aug 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

Other links and lift over

dbSNP: rs405509; hg19: chr19-45408836;