chr13-50708548-G-A

Position:

• chr13-50708548-G-A

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 0.118 in 152,176 control chromosomes in the GnomAD database, including 2,855 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 0.12 (2855 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

Genes affected

(HGNC:):

DLEU7 (HGNC:17567): (deleted in lymphocytic leukemia 7)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.50708548G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000470726.7	n.347-11099G>A		intron_variant		5
DLEU1	ENST00000650910.1	n.386-3990G>A		intron_variant
DLEU7	ENST00000651265.1	n.*469-11970C>T		intron_variant				ENSP00000516017.1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17986 AN: 152058 Hom.: 2854 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0511

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.0393

Gnomad SAS AF: 0.0279

Gnomad FIN AF: 0.0946

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0912

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

GnomAD4 genome AF: 0.118 AC: 18025 AN: 152176 Hom.: 2855 Cov.: 32 AF XY: 0.119 AC XY: 8828 AN XY: 74408

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.0510

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.0394

Gnomad4 SAS AF: 0.0277

Gnomad4 FIN AF: 0.0946

Gnomad4 NFE AF: 0.0102

Gnomad4 OTH AF: 0.0954

Alfa AF: 0.0732 Hom.: 513

Bravo AF: 0.127

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs797510; hg19: chr13-51282684;