13-86530414-C-T

Variant names:

• chr13-86530414-C-T
• rs1328848

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 0.645 in 151,854 control chromosomes in the GnomAD database, including 31,996 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 0.64 (31996 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 3 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 = 0.76 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: 0.644 AC: 97779 AN: 151736 Hom.: 31957 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.645 AC: 97876 AN: 151854 Hom.: 31996 Cov.: 32 AF XY: 0.641 AC XY: 47589 AN XY: 74200

African (AFR) AF: 0.767 AC: 31786 AN: 41458

American (AMR) AF: 0.635 AC: 9695 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1990 AN: 3470

East Asian (EAS) AF: 0.507 AC: 2611 AN: 5146

South Asian (SAS) AF: 0.560 AC: 2698 AN: 4818

European-Finnish (FIN) AF: 0.608 AC: 6406 AN: 10530

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.598 AC: 40549 AN: 67864

Other (OTH) AF: 0.628 AC: 1326 AN: 2112

Alfa AF: 0.596 Hom.: 9441

Bravo AF: 0.653

Asia WGS AF: 0.603 AC: 2092 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.58
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1328848; hg19: chr13-87182669;