rs9288801

Variant names:

• chr3-105351221-A-G
• rs9288801

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 0.662 in 152,084 control chromosomes in the GnomAD database, including 33,634 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 0.66 (33634 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 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: 0.662 AC: 100541 AN: 151966 Hom.: 33610 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.662 AC: 100613 AN: 152084 Hom.: 33634 Cov.: 32 AF XY: 0.662 AC XY: 49196 AN XY: 74358

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.640

Alfa AF: 0.678 Hom.: 7186

Bravo AF: 0.639

Asia WGS AF: 0.611 AC: 2126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9288801; hg19: chr3-105070065;