rs326424

chr3-7840589-G-A

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/exons	MANE	UniProt

Ensembl

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