rs17228531

Variant names:

• chr9-102086218-T-A
• rs17228531

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 0.339 in 148,272 control chromosomes in the GnomAD database, including 8,978 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 0.34 (8978 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 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: 0.339 AC: 50197 AN: 148174 Hom.: 8981 Cov.: 25

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.0675

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.339 AC: 50200 AN: 148272 Hom.: 8978 Cov.: 25 AF XY: 0.336 AC XY: 24230 AN XY: 72090

African (AFR) AF: 0.286 AC: 11482 AN: 40154

American (AMR) AF: 0.281 AC: 4151 AN: 14750

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1450 AN: 3458

East Asian (EAS) AF: 0.0675 AC: 339 AN: 5024

South Asian (SAS) AF: 0.306 AC: 1434 AN: 4686

European-Finnish (FIN) AF: 0.409 AC: 3910 AN: 9552

Middle Eastern (MID) AF: 0.511 AC: 145 AN: 284

European-Non Finnish (NFE) AF: 0.387 AC: 26091 AN: 67416

Other (OTH) AF: 0.349 AC: 713 AN: 2044

Alfa AF: 0.352 Hom.: 1213

Bravo AF: 0.327

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.47
DANN	Benign	0.56
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs17228531; hg19: chr9-104848500;