13-73412717-A-T

Variant names:

• chr13-73412717-A-T
• rs1886452

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 0.651 in 152,102 control chromosomes in the GnomAD database, including 33,192 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 0.65 (33192 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.742 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: 0.651 AC: 98937 AN: 151984 Hom.: 33182 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.651 AC: 98978 AN: 152102 Hom.: 33192 Cov.: 32 AF XY: 0.656 AC XY: 48760 AN XY: 74366

African (AFR) AF: 0.500 AC: 20730 AN: 41464

American (AMR) AF: 0.753 AC: 11520 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2012 AN: 3468

East Asian (EAS) AF: 0.543 AC: 2813 AN: 5178

South Asian (SAS) AF: 0.683 AC: 3291 AN: 4818

European-Finnish (FIN) AF: 0.800 AC: 8458 AN: 10572

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48067 AN: 67994

Other (OTH) AF: 0.656 AC: 1384 AN: 2110

Alfa AF: 0.684 Hom.: 4520

Bravo AF: 0.638

Asia WGS AF: 0.599 AC: 2083 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.3
DANN	Benign	0.68
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs1886452; hg19: chr13-73986854;