rs9381534

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;