rs768539

chr3-46350774-A-Gchr3-46350774-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 0.8 in 152,098 control chromosomes in the GnomAD database, including 49,073 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 (49073 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 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: 0.800 AC: 121592 AN: 151980 Hom.: 49013 Cov.: 30

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.800 AC: 121707 AN: 152098 Hom.: 49073 Cov.: 30 AF XY: 0.801 AC XY: 59589 AN XY: 74348

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.844

Gnomad4 FIN AF: 0.848

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.766

Alfa AF: 0.799 Hom.: 5686

Bravo AF: 0.794

Asia WGS AF: 0.800 AC: 2781 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.6
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs768539; hg19: chr3-46392265;