chr13-50529325-C-G

Variant names:

• chr13-50529325-C-G
• rs536338
• ENST00000460525.6:n.363-3868C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000460525.6(DLEU1):​n.363-3868C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 152,110 control chromosomes in the GnomAD database, including 42,506 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 0.75 (42506 hom., cov: 31)
• Consequence: DLEU1 ENST00000460525.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

Genes affected

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

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 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	ENST00000460525.6	n.363-3868C>G		intron_variant	Intron 3 of 3	1
DLEU1	ENST00000462427.2	n.451+1261C>G		intron_variant	Intron 3 of 3	1
DLEU1	ENST00000470726.7	n.346+95775C>G		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113457 AN: 151992 Hom.: 42476 Cov.: 31

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.746 AC: 113538 AN: 152110 Hom.: 42506 Cov.: 31 AF XY: 0.745 AC XY: 55395 AN XY: 74338

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.799

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.723

Alfa AF: 0.732 Hom.: 5065

Bravo AF: 0.753

Asia WGS AF: 0.705 AC: 2453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs536338; hg19: chr13-51103461;