rs9275686

Variant names:

• chr6-32719793-G-A
• rs9275686

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.305 AC: 12550 AN: 41154

American (AMR) AF: 0.185 AC: 2811 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 851 AN: 3466

East Asian (EAS) AF: 0.139 AC: 715 AN: 5150

South Asian (SAS) AF: 0.120 AC: 576 AN: 4812

European-Finnish (FIN) AF: 0.185 AC: 1941 AN: 10482

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14030 AN: 67896

Other (OTH) AF: 0.230 AC: 484 AN: 2104

Alfa AF: 0.219 Hom.: 9845

Bravo AF: 0.227

Asia WGS AF: 0.131 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.3
DANN	Benign	0.61
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs9275686; hg19: chr6-32687570;