13-50620269-C-T

Variant names:

• chr13-50620269-C-T
• rs573666
• ENST00000469127.6:n.688-18200C>T

Variant summary

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

The ENST00000651397.1(DLEU7):​n.*571+63637G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,004 control chromosomes in the GnomAD database, including 7,379 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 0.30 (7379 hom., cov: 32)
• Consequence: DLEU7 ENST00000651397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• Publications: 13 publications found

Genes affected

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

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

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 = 0.344 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651397.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000469127.6	TSL:5	n.688-18200C>T		intron	N/A
	DLEU1	ENST00000470726.7	TSL:5	n.347-99378C>T		intron	N/A
	DLEU1	ENST00000479420.5	TSL:5	n.560-28321C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46067 AN: 151886 Hom.: 7379 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.303 AC: 46084 AN: 152004 Hom.: 7379 Cov.: 32 AF XY: 0.304 AC XY: 22569 AN XY: 74288

African (AFR) AF: 0.212 AC: 8789 AN: 41462

American (AMR) AF: 0.341 AC: 5203 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1110 AN: 3468

East Asian (EAS) AF: 0.243 AC: 1257 AN: 5176

South Asian (SAS) AF: 0.226 AC: 1088 AN: 4812

European-Finnish (FIN) AF: 0.374 AC: 3943 AN: 10552

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23595 AN: 67948

Other (OTH) AF: 0.331 AC: 699 AN: 2110

Alfa AF: 0.334 Hom.: 37949

Bravo AF: 0.300

Asia WGS AF: 0.226 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.65
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs573666; hg19: chr13-51194405;