13-50162887-G-A

Variant names:

• chr13-50162887-G-A
• rs1750567
• ENST00000461527.7:n.440+79693G>A

Variant summary

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

The ENST00000461527.7(DLEU1):​n.440+79693G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,948 control chromosomes in the GnomAD database, including 23,343 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 0.54 (23343 hom., cov: 31)
• Consequence: DLEU1 ENST00000461527.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377
• Publications: 4 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=-0.56).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000461527.7. 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.442+79693G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000461527.7	TSL:1	n.440+79693G>A		intron	N/A
	DLEU1	ENST00000463474.7	TSL:1	n.440+79693G>A		intron	N/A
	DLEU1	ENST00000468168.6	TSL:1	n.440+79693G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82035 AN: 151830 Hom.: 23348 Cov.: 31

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.540 AC: 82053 AN: 151948 Hom.: 23343 Cov.: 31 AF XY: 0.542 AC XY: 40289 AN XY: 74278

African (AFR) AF: 0.354 AC: 14630 AN: 41382

American (AMR) AF: 0.507 AC: 7741 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2444 AN: 3468

East Asian (EAS) AF: 0.632 AC: 3254 AN: 5150

South Asian (SAS) AF: 0.770 AC: 3717 AN: 4826

European-Finnish (FIN) AF: 0.596 AC: 6295 AN: 10558

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41922 AN: 67964

Other (OTH) AF: 0.556 AC: 1175 AN: 2112

Alfa AF: 0.586 Hom.: 13638

Bravo AF: 0.518

Asia WGS AF: 0.673 AC: 2339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	7.8
DANN	Benign	0.63
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs1750567; hg19: chr13-50737023;