rs17228531

Variant names:

• chr9-102086218-T-A
• rs17228531

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.0675

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.349

Alfa AF: 0.352 Hom.: 1213

Bravo AF: 0.327

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17228531; hg19: chr9-104848500;