13-86590602-C-T

Variant names:

• chr13-86590602-C-T
• rs4773460

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 0.238 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
• Publications: 6 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.450 AC: 18639 AN: 41416

American (AMR) AF: 0.200 AC: 3048 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0522 AC: 181 AN: 3466

East Asian (EAS) AF: 0.156 AC: 806 AN: 5182

South Asian (SAS) AF: 0.114 AC: 547 AN: 4814

European-Finnish (FIN) AF: 0.213 AC: 2243 AN: 10548

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.147 AC: 9981 AN: 67834

Other (OTH) AF: 0.224 AC: 472 AN: 2110

Alfa AF: 0.164 Hom.: 8747

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
PhyloP100		-0.065

Splicing

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

Other links and lift over

dbSNP: rs4773460; hg19: chr13-87242857;