rs9369631

Variant names:

• chr6-46739782-A-G
• rs9369631

Your query was ambiguous. Multiple possible variants found:

• chr6-46739782-A-G
• chr6-46739782-A-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 0.206 in 152,142 control chromosomes in the GnomAD database, including 3,603 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 0.21 (3603 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.46 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: 0.206 AC: 31344 AN: 152024 Hom.: 3590 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.206 AC: 31386 AN: 152142 Hom.: 3603 Cov.: 32 AF XY: 0.214 AC XY: 15909 AN XY: 74372

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.223

Alfa AF: 0.146 Hom.: 374

Bravo AF: 0.198

Asia WGS AF: 0.341 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9369631; hg19: chr6-46707519;