rs9332453

Variant names:

• chr9-81383431-C-T
• rs9332453

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 0.288 in 151,904 control chromosomes in the GnomAD database, including 7,456 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 0.29 (7456 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43742 AN: 151788 Hom.: 7463 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.288 AC: 43717 AN: 151904 Hom.: 7456 Cov.: 33 AF XY: 0.292 AC XY: 21641 AN XY: 74220

African (AFR) AF: 0.111 AC: 4581 AN: 41420

American (AMR) AF: 0.312 AC: 4767 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1315 AN: 3470

East Asian (EAS) AF: 0.150 AC: 776 AN: 5158

South Asian (SAS) AF: 0.454 AC: 2187 AN: 4812

European-Finnish (FIN) AF: 0.341 AC: 3586 AN: 10526

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25277 AN: 67950

Other (OTH) AF: 0.323 AC: 681 AN: 2106

Alfa AF: 0.352 Hom.: 8691

Bravo AF: 0.274

Asia WGS AF: 0.300 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.73
PhyloP100		0.094

Splicing

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

Other links and lift over

dbSNP: rs9332453; hg19: chr9-83998346;