rs9275495

Variant names:

• chr6-32705797-A-T
• rs9275495

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 0.0908 in 151,872 control chromosomes in the GnomAD database, including 810 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 0.091 (810 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0907 AC: 13768 AN: 151756 Hom.: 809 Cov.: 32

Gnomad AFR AF: 0.0368

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0751

Gnomad SAS AF: 0.0677

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0993

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.0908 AC: 13787 AN: 151872 Hom.: 810 Cov.: 32 AF XY: 0.0926 AC XY: 6876 AN XY: 74270

African (AFR) AF: 0.0369 AC: 1534 AN: 41528

American (AMR) AF: 0.179 AC: 2726 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 573 AN: 3448

East Asian (EAS) AF: 0.0753 AC: 390 AN: 5176

South Asian (SAS) AF: 0.0676 AC: 326 AN: 4824

European-Finnish (FIN) AF: 0.109 AC: 1158 AN: 10576

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0993 AC: 6732 AN: 67774

Other (OTH) AF: 0.0903 AC: 191 AN: 2114

Alfa AF: 0.0929 Hom.: 78

Bravo AF: 0.0988

Asia WGS AF: 0.0600 AC: 210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.9
DANN	Benign	0.18
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs9275495; hg19: chr6-32673574;