13-50267187-C-T

Position:

• chr13-50267187-C-T

Variant summary

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

The NR_109974.1(DLEU1):​n.443-123011C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,846 control chromosomes in the GnomAD database, including 17,659 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 0.47 (17659 hom., cov: 31)
• Consequence: DLEU1 NR_109974.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLEU1	NR_109974.1	n.443-123011C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000490577.5	n.1637+109111C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71501 AN: 151728 Hom.: 17669 Cov.: 31

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.471 AC: 71488 AN: 151846 Hom.: 17659 Cov.: 31 AF XY: 0.470 AC XY: 34900 AN XY: 74182

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.488

Alfa AF: 0.521 Hom.: 42308

Bravo AF: 0.457

Asia WGS AF: 0.490 AC: 1703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs806321; hg19: chr13-50841323;