3-86801468-A-G

Position:

• chr3-86801468-A-G

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 0.437 in 145,986 control chromosomes in the GnomAD database, including 14,814 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 0.44 (14814 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.437 AC: 63781 AN: 145980 Hom.: 14803 Cov.: 28

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.437 AC: 63789 AN: 145986 Hom.: 14814 Cov.: 28 AF XY: 0.437 AC XY: 31010 AN XY: 70982

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.444

Alfa AF: 0.265 Hom.: 637

Bravo AF: 0.457

Asia WGS AF: 0.528 AC: 1779 AN: 3374

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.79
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7628864; hg19: chr3-86850618;