rs9837024

Variant names:

• chr3-78402487-A-G
• rs9837024

Your query was ambiguous. Multiple possible variants found:

• chr3-78402487-A-G
• chr3-78402487-A-T

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 0.216 in 151,982 control chromosomes in the GnomAD database, including 4,837 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 0.22 (4837 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.73

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 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: 0.216 AC: 32760 AN: 151864 Hom.: 4821 Cov.: 32

Gnomad AFR AF: 0.0556

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.0806

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.216 AC: 32784 AN: 151982 Hom.: 4837 Cov.: 32 AF XY: 0.223 AC XY: 16556 AN XY: 74260

Gnomad4 AFR AF: 0.0555

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.189

Alfa AF: 0.246 Hom.: 847

Bravo AF: 0.214

Asia WGS AF: 0.364 AC: 1258 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9837024; hg19: chr3-78451637;