rs768539

Variant names:

• chr3-46350774-A-G
• rs768539

Your query was ambiguous. Multiple possible variants found:

• chr3-46350774-A-G
• chr3-46350774-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;