13-50285854-C-T

Variant names:

• chr13-50285854-C-T
• rs806349
• ENST00000461527.7:n.555+10808C>T

Variant summary

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

The ENST00000461527.7(DLEU1):​n.555+10808C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,888 control chromosomes in the GnomAD database, including 13,957 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 0.41 (13957 hom., cov: 31)
• Consequence: DLEU1 ENST00000461527.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLEU1	NR_109974.1	n.443-104344C>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000461527.7	n.555+10808C>T		intron_variant	Intron 3 of 5	1
DLEU1	ENST00000463474.7	n.441-52822C>T		intron_variant	Intron 2 of 5	1
DLEU1	ENST00000468168.5	n.441-104344C>T		intron_variant	Intron 2 of 5	1

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62844 AN: 151770 Hom.: 13968 Cov.: 31

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.414 AC: 62835 AN: 151888 Hom.: 13957 Cov.: 31 AF XY: 0.412 AC XY: 30571 AN XY: 74248

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.430

Alfa AF: 0.453 Hom.: 8805

Bravo AF: 0.403

Asia WGS AF: 0.489 AC: 1699 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs806349; hg19: chr13-50859990;