rs9332422

Variant names:

• chr2-123088658-A-C
• rs9332422

Your query was ambiguous. Multiple possible variants found:

• chr2-123088658-A-C
• chr2-123088658-A-G
• chr2-123088658-A-T

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 0.406 in 151,962 control chromosomes in the GnomAD database, including 12,893 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 0.41 (12893 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.508 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: 0.406 AC: 61676 AN: 151844 Hom.: 12898 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.406 AC: 61677 AN: 151962 Hom.: 12893 Cov.: 32 AF XY: 0.408 AC XY: 30304 AN XY: 74280

African (AFR) AF: 0.294 AC: 12178 AN: 41434

American (AMR) AF: 0.439 AC: 6690 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1578 AN: 3472

East Asian (EAS) AF: 0.524 AC: 2699 AN: 5148

South Asian (SAS) AF: 0.464 AC: 2236 AN: 4822

European-Finnish (FIN) AF: 0.439 AC: 4629 AN: 10544

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30213 AN: 67970

Other (OTH) AF: 0.444 AC: 937 AN: 2110

Alfa AF: 0.270 Hom.: 640

Bravo AF: 0.404

Asia WGS AF: 0.487 AC: 1688 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.62
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9332422; hg19: chr2-123846234;