chr3-105351221-A-G

Variant names:

• chr3-105351221-A-G
• rs9288801

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 0.662 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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

African (AFR) AF: 0.652 AC: 27074 AN: 41510

American (AMR) AF: 0.507 AC: 7735 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2470 AN: 3470

East Asian (EAS) AF: 0.571 AC: 2952 AN: 5168

South Asian (SAS) AF: 0.680 AC: 3271 AN: 4810

European-Finnish (FIN) AF: 0.780 AC: 8257 AN: 10590

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46764 AN: 67956

Other (OTH) AF: 0.640 AC: 1350 AN: 2110

Alfa AF: 0.677 Hom.: 7356

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
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs9288801; hg19: chr3-105070065;