rs326424

Variant names:

• chr3-7840589-G-A
• rs326424

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 0.797 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.797 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

Gnomad4 AFR AF: 0.881

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.816

Alfa AF: 0.792 Hom.: 5947

Bravo AF: 0.803

Asia WGS AF: 0.728 AC: 2534 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs326424; hg19: chr3-7882276;