rs9833097

Variant names:

• chr3-12437318-G-A
• rs9833097

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 0.113 in 152,092 control chromosomes in the GnomAD database, including 1,138 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 0.11 (1138 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.19 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: 0.113 AC: 17220 AN: 151974 Hom.: 1139 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0860

Gnomad FIN AF: 0.0947

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.113 AC: 17239 AN: 152092 Hom.: 1138 Cov.: 32 AF XY: 0.113 AC XY: 8378 AN XY: 74342

African (AFR) AF: 0.109 AC: 4503 AN: 41474

American (AMR) AF: 0.196 AC: 2998 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 422 AN: 3464

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5184

South Asian (SAS) AF: 0.0863 AC: 415 AN: 4808

European-Finnish (FIN) AF: 0.0947 AC: 1004 AN: 10602

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7253 AN: 67974

Other (OTH) AF: 0.130 AC: 274 AN: 2110

Alfa AF: 0.118 Hom.: 2622

Bravo AF: 0.124

Asia WGS AF: 0.0640 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.40
DANN	Benign	0.39
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs9833097; hg19: chr3-12478817;