3-86797628-G-T

Position:

• chr3-86797628-G-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 0.445 in 151,880 control chromosomes in the GnomAD database, including 15,780 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 0.45 (15780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 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: 0.445 AC: 67556 AN: 151762 Hom.: 15751 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.445 AC: 67622 AN: 151880 Hom.: 15780 Cov.: 32 AF XY: 0.445 AC XY: 33014 AN XY: 74204

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.450

Alfa AF: 0.362 Hom.: 1470

Bravo AF: 0.465

Asia WGS AF: 0.531 AC: 1845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1437049; hg19: chr3-86846778;