13-86043963-A-G

Variant names:

• chr13-86043963-A-G
• rs9319189

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.854 AC: 35441 AN: 41482

American (AMR) AF: 0.593 AC: 9055 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1968 AN: 3470

East Asian (EAS) AF: 0.632 AC: 3247 AN: 5140

South Asian (SAS) AF: 0.677 AC: 3261 AN: 4814

European-Finnish (FIN) AF: 0.768 AC: 8111 AN: 10568

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44870 AN: 67968

Other (OTH) AF: 0.675 AC: 1422 AN: 2108

Alfa AF: 0.654 Hom.: 52879

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
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs9319189; hg19: chr13-86618098;