13-50519978-T-G

Variant names:

• chr13-50519978-T-G
• rs9316500
• ENST00000460525.6:n.363-13215T>G

Variant summary

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

The ENST00000460525.6(DLEU1):​n.363-13215T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,074 control chromosomes in the GnomAD database, including 6,736 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 0.29 (6736 hom., cov: 32)
• Consequence: DLEU1 ENST00000460525.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 21 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 (EAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000460525.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	NR_109974.1		n.786-7888T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000460525.6	TSL:1	n.363-13215T>G		intron	N/A
	DLEU1	ENST00000462427.2	TSL:1	n.253-7888T>G		intron	N/A
	DLEU1	ENST00000463474.7	TSL:1	n.849-7888T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43601 AN: 151956 Hom.: 6732 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.287 AC: 43627 AN: 152074 Hom.: 6736 Cov.: 32 AF XY: 0.282 AC XY: 20980 AN XY: 74378

African (AFR) AF: 0.251 AC: 10398 AN: 41496

American (AMR) AF: 0.227 AC: 3474 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1310 AN: 3470

East Asian (EAS) AF: 0.637 AC: 3289 AN: 5162

South Asian (SAS) AF: 0.308 AC: 1484 AN: 4814

European-Finnish (FIN) AF: 0.195 AC: 2067 AN: 10592

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20481 AN: 67950

Other (OTH) AF: 0.291 AC: 615 AN: 2110

Alfa AF: 0.300 Hom.: 31237

Bravo AF: 0.289

Asia WGS AF: 0.415 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.73
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs9316500; hg19: chr13-51094114;