rs9837024

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;