rs9990343

Variant names:

• chr3-46298321-A-G
• rs9990343

Your query was ambiguous. Multiple possible variants found:

• chr3-46298321-A-G
• chr3-46298321-A-T

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 0.487 in 151,848 control chromosomes in the GnomAD database, including 18,598 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 0.49 (18598 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 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: 0.488 AC: 73981 AN: 151730 Hom.: 18593 Cov.: 30

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.487 AC: 74016 AN: 151848 Hom.: 18598 Cov.: 30 AF XY: 0.485 AC XY: 35956 AN XY: 74188

African (AFR) AF: 0.516 AC: 21369 AN: 41380

American (AMR) AF: 0.377 AC: 5752 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1635 AN: 3470

East Asian (EAS) AF: 0.125 AC: 644 AN: 5160

South Asian (SAS) AF: 0.430 AC: 2069 AN: 4814

European-Finnish (FIN) AF: 0.592 AC: 6234 AN: 10530

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34823 AN: 67918

Other (OTH) AF: 0.436 AC: 919 AN: 2106

Alfa AF: 0.488 Hom.: 66721

Bravo AF: 0.472

Asia WGS AF: 0.296 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.52
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs9990343; hg19: chr3-46339812;