13-50519978-T-G

Position:

• chr13-50519978-T-G

Variant summary

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

The ENST00000651397.1(DLEU7):​n.*2086A>C 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 0.287 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: DLEU7 ENST00000651397.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383

Genes affected

DLEU1 (HGNC:):

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLEU1	NR_109974.1	n.786-7888T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000460525.6	n.363-13215T>G		intron_variant		1
DLEU1	ENST00000462427.2	n.253-7888T>G		intron_variant		1
DLEU1	ENST00000463474.7	n.849-7888T>G		intron_variant		1

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

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.291

Alfa AF: 0.303 Hom.: 16059

Bravo AF: 0.289

Asia WGS AF: 0.415 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
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: rs9316500; hg19: chr13-51094114;