rs2251622

Variant names:

• chr9-88208691-T-A
• rs2251622

Your query was ambiguous. Multiple possible variants found:

• chr9-88208691-T-A
• chr9-88208691-T-C

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 0.588 in 152,094 control chromosomes in the GnomAD database, including 30,306 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 0.59 (30306 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 9 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 (NFE) allele frequency at 95% confidence interval = 0.75 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: 0.588 AC: 89415 AN: 151976 Hom.: 30298 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.588 AC: 89435 AN: 152094 Hom.: 30306 Cov.: 32 AF XY: 0.591 AC XY: 43916 AN XY: 74338

African (AFR) AF: 0.246 AC: 10198 AN: 41484

American (AMR) AF: 0.617 AC: 9419 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2739 AN: 3466

East Asian (EAS) AF: 0.373 AC: 1929 AN: 5174

South Asian (SAS) AF: 0.678 AC: 3269 AN: 4822

European-Finnish (FIN) AF: 0.780 AC: 8244 AN: 10574

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51394 AN: 67990

Other (OTH) AF: 0.657 AC: 1388 AN: 2112

Alfa AF: 0.657 Hom.: 4424

Bravo AF: 0.560

Asia WGS AF: 0.535 AC: 1859 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	7.5
DANN	Benign	0.73
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2251622; hg19: chr9-90823606;