chr13-50636244-C-T

Variant names:

• chr13-50636244-C-T
• rs7991818
• ENST00000469127.6:n.688-2225C>T

Variant summary

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

The ENST00000469127.6(DLEU1):​n.688-2225C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 151,986 control chromosomes in the GnomAD database, including 2,559 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 0.16 (2559 hom., cov: 31)
• Consequence: DLEU1 ENST00000469127.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 5 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000469127.6. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000469127.6	TSL:5	n.688-2225C>T		intron	N/A
	DLEU1	ENST00000470726.7	TSL:5	n.347-83403C>T		intron	N/A
	DLEU1	ENST00000479420.5	TSL:5	n.560-12346C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24709 AN: 151868 Hom.: 2555 Cov.: 31

Gnomad AFR AF: 0.0431

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.0718

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.163 AC: 24718 AN: 151986 Hom.: 2559 Cov.: 31 AF XY: 0.164 AC XY: 12156 AN XY: 74266

African (AFR) AF: 0.0433 AC: 1798 AN: 41504

American (AMR) AF: 0.157 AC: 2394 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 602 AN: 3472

East Asian (EAS) AF: 0.132 AC: 681 AN: 5150

South Asian (SAS) AF: 0.0708 AC: 341 AN: 4818

European-Finnish (FIN) AF: 0.296 AC: 3122 AN: 10550

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15127 AN: 67912

Other (OTH) AF: 0.183 AC: 387 AN: 2112

Alfa AF: 0.201 Hom.: 10359

Bravo AF: 0.153

Asia WGS AF: 0.0750 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.56
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs7991818; hg19: chr13-51210380;