13-50375812-G-T

Variant names:

• chr13-50375812-G-T
• rs12864797
• ENST00000461527.7:n.556-39277G>T

Variant summary

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

The ENST00000461527.7(DLEU1):​n.556-39277G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0798 in 151,892 control chromosomes in the GnomAD database, including 541 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 0.080 (541 hom., cov: 29)
• Consequence: DLEU1 ENST00000461527.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.860
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0897 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	NR_109974.1		n.443-14386G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000461527.7	TSL:1	n.556-39277G>T		intron	N/A
	DLEU1	ENST00000463357.5	TSL:1	n.181-14386G>T		intron	N/A
	DLEU1	ENST00000463474.7	TSL:1	n.599+36978G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0797 AC: 12102 AN: 151774 Hom.: 534 Cov.: 29

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0659

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.0835

Gnomad FIN AF: 0.0855

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0916

Gnomad OTH AF: 0.0764

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

GnomAD4 genome AF: 0.0798 AC: 12120 AN: 151892 Hom.: 541 Cov.: 29 AF XY: 0.0786 AC XY: 5838 AN XY: 74242

African (AFR) AF: 0.0700 AC: 2895 AN: 41372

American (AMR) AF: 0.0656 AC: 1000 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 352 AN: 3468

East Asian (EAS) AF: 0.0114 AC: 59 AN: 5172

South Asian (SAS) AF: 0.0836 AC: 402 AN: 4808

European-Finnish (FIN) AF: 0.0855 AC: 903 AN: 10558

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0916 AC: 6228 AN: 67972

Other (OTH) AF: 0.0856 AC: 180 AN: 2102

Alfa AF: 0.0815 Hom.: 655

Bravo AF: 0.0761

Asia WGS AF: 0.0810 AC: 282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.0
DANN	Benign	0.48
PhyloP100		0.86

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12864797;

hg19: chr13-50949948;