rs9275686

Variant names:

• chr6-32719793-G-A
• rs9275686

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 0.225 in 151,452 control chromosomes in the GnomAD database, including 4,048 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 0.23 (4048 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 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: 0.225 AC: 34069 AN: 151332 Hom.: 4038 Cov.: 28

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.225 AC: 34100 AN: 151452 Hom.: 4048 Cov.: 28 AF XY: 0.220 AC XY: 16248 AN XY: 73972

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.230

Alfa AF: 0.210 Hom.: 2135

Bravo AF: 0.227

Asia WGS AF: 0.131 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9275686; hg19: chr6-32687570;