rs9568401

Variant names:

• chr13-50386160-C-G
• rs9568401
• ENST00000461527.7:n.556-28929C>G

Variant summary

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

The ENST00000461527.7(DLEU1):​n.556-28929C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,208 control chromosomes in the GnomAD database, including 2,341 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 0.13 (2341 hom., cov: 34)
• Consequence: DLEU1 ENST00000461527.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 4 publications found

Genes affected

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

ENSG00000286191 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLEU1	NR_109974.1	n.443-4038C>G		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000461527.7	n.556-28929C>G		intron_variant	Intron 3 of 5	1
DLEU1	ENST00000463357.5	n.181-4038C>G		intron_variant	Intron 1 of 1	1
DLEU1	ENST00000463474.7	n.600-47253C>G		intron_variant	Intron 3 of 5	1

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19358 AN: 152090 Hom.: 2339 Cov.: 34

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0978

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.127 AC: 19361 AN: 152208 Hom.: 2341 Cov.: 34 AF XY: 0.132 AC XY: 9787 AN XY: 74414

African (AFR) AF: 0.100 AC: 4155 AN: 41542

American (AMR) AF: 0.0976 AC: 1491 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 386 AN: 3468

East Asian (EAS) AF: 0.743 AC: 3843 AN: 5170

South Asian (SAS) AF: 0.201 AC: 971 AN: 4824

European-Finnish (FIN) AF: 0.106 AC: 1119 AN: 10602

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6930 AN: 68000

Other (OTH) AF: 0.130 AC: 275 AN: 2116

Alfa AF: 0.106 Hom.: 130

Bravo AF: 0.131

Asia WGS AF: 0.362 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.42
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs9568401; hg19: chr13-50960296;