rs9990333

Variant names:

• chr3-196100334-C-T
• rs9990333

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 0.418 in 150,862 control chromosomes in the GnomAD database, including 13,775 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 0.42 (13775 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 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: 0.419 AC: 63092 AN: 150744 Hom.: 13771 Cov.: 28

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.0121

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.418 AC: 63113 AN: 150862 Hom.: 13775 Cov.: 28 AF XY: 0.411 AC XY: 30294 AN XY: 73622

African (AFR) AF: 0.435 AC: 17838 AN: 40962

American (AMR) AF: 0.336 AC: 5088 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1692 AN: 3462

East Asian (EAS) AF: 0.0121 AC: 62 AN: 5106

South Asian (SAS) AF: 0.403 AC: 1926 AN: 4782

European-Finnish (FIN) AF: 0.387 AC: 4018 AN: 10376

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 30955 AN: 67730

Other (OTH) AF: 0.426 AC: 896 AN: 2104

Alfa AF: 0.440 Hom.: 47462

Bravo AF: 0.411

Asia WGS AF: 0.204 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.50
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs9990333; hg19: chr3-195827205;