rs9889296

Positions:

• chr17-34243528-G-A

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 0.332 in 152,110 control chromosomes in the GnomAD database, including 8,851 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 0.33 (8851 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50424 AN: 151992 Hom.: 8829 Cov.: 33

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.332 AC: 50491 AN: 152110 Hom.: 8851 Cov.: 33 AF XY: 0.339 AC XY: 25235 AN XY: 74344

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.321

Alfa AF: 0.296 Hom.: 847

Bravo AF: 0.342

Asia WGS AF: 0.457 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9889296; hg19: chr17-32570547;