rs3118650

Variant names:

• chr13-50455188-A-G
• rs3118650
• ENST00000460525.6:n.251+21638A>G

Variant summary

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

The ENST00000460525.6(DLEU1):​n.251+21638A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0767 in 150,790 control chromosomes in the GnomAD database, including 487 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 0.077 (487 hom., cov: 32)
• Consequence: DLEU1 ENST00000460525.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLEU1	NR_109974.1	n.674+21638A>G		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000460525.6	n.251+21638A>G		intron_variant	Intron 2 of 3	1
DLEU1	ENST00000461527.7	n.807+21638A>G		intron_variant	Intron 5 of 5	1
DLEU1	ENST00000462427.2	n.252+21638A>G		intron_variant	Intron 2 of 3	1

Frequencies

GnomAD3 genomes AF: 0.0766 AC: 11544 AN: 150674 Hom.: 480 Cov.: 32

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.0640

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0884

Gnomad FIN AF: 0.0490

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0895

Gnomad OTH AF: 0.0861

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

GnomAD4 genome AF: 0.0767 AC: 11561 AN: 150790 Hom.: 487 Cov.: 32 AF XY: 0.0746 AC XY: 5491 AN XY: 73636

African (AFR) AF: 0.0695 AC: 2862 AN: 41200

American (AMR) AF: 0.0638 AC: 968 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 404 AN: 3456

East Asian (EAS) AF: 0.0140 AC: 64 AN: 4586

South Asian (SAS) AF: 0.0883 AC: 420 AN: 4756

European-Finnish (FIN) AF: 0.0490 AC: 516 AN: 10538

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0894 AC: 6064 AN: 67794

Other (OTH) AF: 0.0952 AC: 199 AN: 2090

Alfa AF: 0.0870 Hom.: 344

Bravo AF: 0.0755

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.49
DANN	Benign	0.63
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3118650; hg19: chr13-51029324;