chr13-50082446-T-A

Position:

• chr13-50082446-T-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_109974.1(DLEU1):​n.278T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 470,932 control chromosomes in the GnomAD database, including 11,976 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 0.20 (3597 hom., cov: 32)
  • Exomes 𝑓: 0.22 (8379 hom.)
• Consequence: DLEU1 NR_109974.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300

Genes affected

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

(HGNC:):

DLEU2 (HGNC:13748): (deleted in lymphocytic leukemia 2) This locus represents a microRNA host gene and also produces long alternatively spliced non-coding RNAs. This genome region was observed to be deleted or epigenetically suppressed in leukemia, and was implicated as a negative regulator of cell proliferation. However, an alternative transcript produced at this locus was also found to promote progression through the cell cycle via angiotensin I converting enzyme 2 and cyclin D1. [provided by RefSeq, Dec 2017]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLEU1	NR_109974.1	n.278T>A		non_coding_transcript_exon_variant	1/7
DLEU2	NR_152566.1	n.241-6793A>T		intron_variant, non_coding_transcript_variant
DLEU1	NR_002605.2	n.278T>A		non_coding_transcript_exon_variant	1/2
DLEU1	NR_109973.1	n.278T>A		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLEU1	ENST00000490577.5	n.276T>A		non_coding_transcript_exon_variant	1/6	5
	ENST00000618107.1	n.152T>A		non_coding_transcript_exon_variant	1/1
DLEU2	ENST00000621282.4	n.241-6793A>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30126 AN: 152076 Hom.: 3599 Cov.: 32

Gnomad AFR AF: 0.0789

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.185

GnomAD3 exomes AF: 0.219 AC: 33250 AN: 151586 Hom.: 3985 AF XY: 0.216 AC XY: 17621 AN XY: 81434

Gnomad AFR exome AF: 0.0741

Gnomad AMR exome AF: 0.204

Gnomad ASJ exome AF: 0.211

Gnomad EAS exome AF: 0.342

Gnomad SAS exome AF: 0.118

Gnomad FIN exome AF: 0.250

Gnomad NFE exome AF: 0.253

Gnomad OTH exome AF: 0.211

GnomAD4 exome AF: 0.220 AC: 69964 AN: 318738 Hom.: 8379 Cov.: 0 AF XY: 0.212 AC XY: 38249 AN XY: 180048

Gnomad4 AFR exome AF: 0.0810

Gnomad4 AMR exome AF: 0.203

Gnomad4 ASJ exome AF: 0.214

Gnomad4 EAS exome AF: 0.350

Gnomad4 SAS exome AF: 0.120

Gnomad4 FIN exome AF: 0.252

Gnomad4 NFE exome AF: 0.255

Gnomad4 OTH exome AF: 0.223

GnomAD4 genome AF: 0.198 AC: 30141 AN: 152194 Hom.: 3597 Cov.: 32 AF XY: 0.197 AC XY: 14679 AN XY: 74414

Gnomad4 AFR AF: 0.0790

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.187

Alfa AF: 0.162 Hom.: 494

Bravo AF: 0.193

Asia WGS AF: 0.209 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	4.9
DANN	Benign	0.78
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2066575; hg19: chr13-50656582; COSMIC: COSV52400674;