chr13-86043963-A-G

Position:

• chr13-86043963-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 0.712 in 152,018 control chromosomes in the GnomAD database, including 39,288 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 0.71 (39288 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.86043963A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108058 AN: 151900 Hom.: 39227 Cov.: 31

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.712 AC: 108185 AN: 152018 Hom.: 39288 Cov.: 31 AF XY: 0.714 AC XY: 53020 AN XY: 74304

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.675

Alfa AF: 0.647 Hom.: 40081

Bravo AF: 0.702

Asia WGS AF: 0.702 AC: 2442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9319189; hg19: chr13-86618098;