3-78402487-A-G

Variant names:

• chr3-78402487-A-G
• rs9837024

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 0.216 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0555 AC: 2306 AN: 41534

American (AMR) AF: 0.366 AC: 5573 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 447 AN: 3470

East Asian (EAS) AF: 0.527 AC: 2701 AN: 5130

South Asian (SAS) AF: 0.296 AC: 1427 AN: 4826

European-Finnish (FIN) AF: 0.316 AC: 3333 AN: 10546

Middle Eastern (MID) AF: 0.0799 AC: 23 AN: 288

European-Non Finnish (NFE) AF: 0.242 AC: 16423 AN: 67946

Other (OTH) AF: 0.189 AC: 397 AN: 2102

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
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs9837024; hg19: chr3-78451637;