13-73412717-A-T

Position:

• chr13-73412717-A-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 0.651 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.73412717A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.800

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.656

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1886452; hg19: chr13-73986854;