3-7840589-G-A

Variant names:

• chr3-7840589-G-A
• rs326424

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 0.797 in 152,096 control chromosomes in the GnomAD database, including 48,646 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 0.80 (48646 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.797 AC: 121159 AN: 151978 Hom.: 48603 Cov.: 31

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.797 AC: 121257 AN: 152096 Hom.: 48646 Cov.: 31 AF XY: 0.796 AC XY: 59173 AN XY: 74330

African (AFR) AF: 0.881 AC: 36587 AN: 41506

American (AMR) AF: 0.780 AC: 11920 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2654 AN: 3472

East Asian (EAS) AF: 0.619 AC: 3189 AN: 5156

South Asian (SAS) AF: 0.735 AC: 3538 AN: 4814

European-Finnish (FIN) AF: 0.776 AC: 8208 AN: 10572

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52488 AN: 67992

Other (OTH) AF: 0.816 AC: 1720 AN: 2108

Alfa AF: 0.795 Hom.: 6253

Bravo AF: 0.803

Asia WGS AF: 0.728 AC: 2534 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs326424; hg19: chr3-7882276;