13-50411982-T-C

Variant names:

• chr13-50411982-T-C
• rs201789
• ENST00000461527.7:n.556-3107T>C

Variant summary

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

The ENST00000461527.7(DLEU1):​n.556-3107T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 152,144 control chromosomes in the GnomAD database, including 35,922 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 0.68 (35922 hom., cov: 33)
• Consequence: DLEU1 ENST00000461527.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 9 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.734 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.537-21431T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000461527.7	TSL:1	n.556-3107T>C		intron	N/A
	DLEU1	ENST00000463474.7	TSL:1	n.600-21431T>C		intron	N/A
	DLEU1	ENST00000468168.6	TSL:1	n.535-21431T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102999 AN: 152026 Hom.: 35910 Cov.: 33

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.677 AC: 103041 AN: 152144 Hom.: 35922 Cov.: 33 AF XY: 0.676 AC XY: 50265 AN XY: 74390

African (AFR) AF: 0.588 AC: 24373 AN: 41482

American (AMR) AF: 0.739 AC: 11296 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2564 AN: 3470

East Asian (EAS) AF: 0.209 AC: 1086 AN: 5188

South Asian (SAS) AF: 0.601 AC: 2890 AN: 4812

European-Finnish (FIN) AF: 0.779 AC: 8265 AN: 10606

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50250 AN: 67988

Other (OTH) AF: 0.684 AC: 1443 AN: 2110

Alfa AF: 0.707 Hom.: 80890

Bravo AF: 0.668

Asia WGS AF: 0.461 AC: 1604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.64
PhyloP100		-0.13

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: rs201789;

hg19: chr13-50986118;