13-86590602-C-T

Position:

• chr13-86590602-C-T

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 0.238 in 151,828 control chromosomes in the GnomAD database, including 5,719 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 0.24 (5719 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36001 AN: 151710 Hom.: 5688 Cov.: 33

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.238 AC: 36085 AN: 151828 Hom.: 5719 Cov.: 33 AF XY: 0.236 AC XY: 17498 AN XY: 74186

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.0522

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.224

Alfa AF: 0.139 Hom.: 2532

Bravo AF: 0.248

Asia WGS AF: 0.188 AC: 650 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4773460; hg19: chr13-87242857;