ENST00000461527.7:n.441-13353C>T

Variant names:

• chr13-50261579-C-T
• rs2762051
• ENST00000461527.7:n.441-13353C>T

Variant summary

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

The ENST00000461527.7(DLEU1):​n.441-13353C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,240 control chromosomes in the GnomAD database, including 2,067 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 0.15 (2067 hom., cov: 32)
• Consequence: DLEU1 ENST00000461527.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 30 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLEU1	NR_109974.1	n.443-128619C>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000461527.7	n.441-13353C>T		intron_variant	Intron 2 of 5	1
DLEU1	ENST00000463474.7	n.441-77097C>T		intron_variant	Intron 2 of 5	1
DLEU1	ENST00000468168.6	n.441-128619C>T		intron_variant	Intron 2 of 5	1

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22872 AN: 152122 Hom.: 2060 Cov.: 32

Gnomad AFR AF: 0.0724

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0252

Gnomad SAS AF: 0.0942

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.150 AC: 22895 AN: 152240 Hom.: 2067 Cov.: 32 AF XY: 0.151 AC XY: 11239 AN XY: 74426

African (AFR) AF: 0.0724 AC: 3007 AN: 41550

American (AMR) AF: 0.225 AC: 3443 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 632 AN: 3470

East Asian (EAS) AF: 0.0248 AC: 129 AN: 5194

South Asian (SAS) AF: 0.0944 AC: 456 AN: 4828

European-Finnish (FIN) AF: 0.209 AC: 2219 AN: 10594

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.183 AC: 12464 AN: 67992

Other (OTH) AF: 0.161 AC: 340 AN: 2114

Alfa AF: 0.172 Hom.: 11363

Bravo AF: 0.150

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.59
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2762051; hg19: chr13-50835715;