rs9288801

chr3-105351221-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;