13-86534027-G-A

Variant names:

• chr13-86534027-G-A
• rs9301535

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 0.188 in 151,878 control chromosomes in the GnomAD database, including 2,986 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 0.19 (2986 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 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: 0.188 AC: 28509 AN: 151758 Hom.: 2966 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.188 AC: 28576 AN: 151878 Hom.: 2986 Cov.: 32 AF XY: 0.188 AC XY: 13988 AN XY: 74214

African (AFR) AF: 0.280 AC: 11621 AN: 41430

American (AMR) AF: 0.183 AC: 2788 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0522 AC: 181 AN: 3470

East Asian (EAS) AF: 0.148 AC: 761 AN: 5146

South Asian (SAS) AF: 0.109 AC: 526 AN: 4818

European-Finnish (FIN) AF: 0.213 AC: 2244 AN: 10540

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.146 AC: 9893 AN: 67924

Other (OTH) AF: 0.190 AC: 399 AN: 2102

Alfa AF: 0.148 Hom.: 928

Bravo AF: 0.191

Asia WGS AF: 0.180 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.66
DANN	Benign	0.52
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs9301535; hg19: chr13-87186282;