chr13-50708548-G-A

Variant names:

• chr13-50708548-G-A
• rs797510
• ENST00000470726.7:n.347-11099G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000470726.7(DLEU1):​n.347-11099G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: DLEU1 ENST00000470726.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 1 publications found

Genes affected

DLEU1 (HGNC:13747): (deleted in lymphocytic leukemia 1)

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

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000470726.7	n.347-11099G>A		intron_variant	Intron 3 of 5	5
DLEU1	ENST00000650910.1	n.386-3990G>A		intron_variant	Intron 1 of 3
DLEU7	ENST00000651265.1	n.*469-11970C>T		intron_variant	Intron 3 of 3			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

African (AFR) AF: 0.361 AC: 14965 AN: 41486

American (AMR) AF: 0.0510 AC: 780 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00807 AC: 28 AN: 3470

East Asian (EAS) AF: 0.0394 AC: 204 AN: 5182

South Asian (SAS) AF: 0.0277 AC: 134 AN: 4830

European-Finnish (FIN) AF: 0.0946 AC: 1002 AN: 10592

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0102 AC: 691 AN: 68010

Other (OTH) AF: 0.0954 AC: 201 AN: 2106

Alfa AF: 0.0407 Hom.: 1353

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
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs797510; hg19: chr13-51282684;