rs439401

chr19-44911194-T-C

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 0.67 in 152,334 control chromosomes in the GnomAD database, including 35,521 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 0.67 (35477 hom., cov: 33)
  • Exomes 𝑓: 0.72 (44 hom.)
• Consequence: Unknown
• Clinical Significance: drug response no assertion criteria provided O:1
• Conservation: PhyloP100: -0.0130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 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: 0.670 AC: 101854 AN: 152046 Hom.: 35420 Cov.: 33

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.639

GnomAD4 exome AF: 0.718 AC: 122 AN: 170 Hom.: 44 Cov.: 0 AF XY: 0.714 AC XY: 90 AN XY: 126

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.750

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.722

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.670 AC: 101979 AN: 152164 Hom.: 35477 Cov.: 33 AF XY: 0.667 AC XY: 49620 AN XY: 74390

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.643

Alfa AF: 0.621 Hom.: 66547

Bravo AF: 0.663

Asia WGS AF: 0.540 AC: 1880 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	-0.66
Cadd	Benign	4.9
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs439401; hg19: chr19-45414451;