ENST00000400393.3:c.459+21307C>G

Variant names:

• chr13-50821881-G-C
• rs9535499
• ENST00000400393.3:c.459+21307C>G

Variant summary

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

The ENST00000400393.3(DLEU7):​c.459+21307C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,922 control chromosomes in the GnomAD database, including 28,220 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 0.60 (28220 hom., cov: 31)
• Consequence: DLEU7 ENST00000400393.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569
• Publications: 7 publications found

Genes affected

DLEU7 (HGNC:17567): (deleted in lymphocytic leukemia 7)

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

DLEU7-AS1 (HGNC:39966): (DLEU7 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLEU7	NM_198989.3	c.459+21307C>G		intron_variant	Intron 1 of 1		NP_945340.2
DLEU7-AS1	NR_046551.1	n.371+3289G>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLEU7	ENST00000400393.3	c.459+21307C>G		intron_variant	Intron 1 of 1	1		ENSP00000420976.1
DLEU1	ENST00000413510.4	n.371+3289G>C		intron_variant	Intron 3 of 4	1
DLEU7	ENST00000651265.1	n.*468+1312C>G		intron_variant	Intron 3 of 3			ENSP00000516017.1

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91574 AN: 151806 Hom.: 28185 Cov.: 31

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.603 AC: 91653 AN: 151922 Hom.: 28220 Cov.: 31 AF XY: 0.600 AC XY: 44544 AN XY: 74212

African (AFR) AF: 0.734 AC: 30407 AN: 41444

American (AMR) AF: 0.540 AC: 8246 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2005 AN: 3470

East Asian (EAS) AF: 0.513 AC: 2642 AN: 5154

South Asian (SAS) AF: 0.402 AC: 1934 AN: 4810

European-Finnish (FIN) AF: 0.600 AC: 6323 AN: 10530

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38240 AN: 67938

Other (OTH) AF: 0.602 AC: 1270 AN: 2108

Alfa AF: 0.449 Hom.: 1155

Bravo AF: 0.606

Asia WGS AF: 0.470 AC: 1636 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.59
PhyloP100		-0.57
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9535499; hg19: chr13-51396017;