rs9381534

Variant names:

• chr6-47345755-G-A
• rs9381534

Your query was ambiguous. Multiple possible variants found:

• chr6-47345755-G-A
• chr6-47345755-G-T

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 0.115 in 152,056 control chromosomes in the GnomAD database, including 2,152 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (2152 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17445 AN: 151938 Hom.: 2140 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.0599

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0551

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0425

Gnomad OTH AF: 0.103

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.115 AC: 17500 AN: 152056 Hom.: 2152 Cov.: 31 AF XY: 0.122 AC XY: 9033 AN XY: 74302

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.0599

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.0551

Gnomad4 NFE AF: 0.0425

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0303 Hom.: 11

Bravo AF: 0.135

Asia WGS AF: 0.354 AC: 1227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.9
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9381534; hg19: chr6-47313491;