13-86836360-G-A

Position:

• chr13-86836360-G-A

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 0.272 in 151,994 control chromosomes in the GnomAD database, including 5,827 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 0.27 (5827 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.86836360G>A		intergenic_region
LOC105370300	XR_931621.3	n.361+41384G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41331 AN: 151876 Hom.: 5817 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.272 AC: 41368 AN: 151994 Hom.: 5827 Cov.: 32 AF XY: 0.276 AC XY: 20471 AN XY: 74290

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.258

Alfa AF: 0.243 Hom.: 572

Bravo AF: 0.281

Asia WGS AF: 0.371 AC: 1294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4495987; hg19: chr13-87488615;