13-50542765-G-T

Variant names:

• chr13-50542765-G-T
• rs3118914
• ENST00000469127.6:n.585+37085G>T

Variant summary

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

The ENST00000651397.1(DLEU7):​n.*572-16758C>A 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 151,900 control chromosomes in the GnomAD database, including 2,261 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 (2261 hom., cov: 31)
• Consequence: DLEU7 ENST00000651397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.616
• Publications: 35 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 = 0.208 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.585+37085G>T		intron	N/A
	DLEU1	ENST00000470726.7	TSL:5	n.346+109215G>T		intron	N/A
	DLEU1	ENST00000479420.5	TSL:5	n.458-46710G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22830 AN: 151780 Hom.: 2262 Cov.: 31

Gnomad AFR AF: 0.0352

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0193

Gnomad SAS AF: 0.0874

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.154

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.150 AC: 22816 AN: 151900 Hom.: 2261 Cov.: 31 AF XY: 0.151 AC XY: 11185 AN XY: 74220

African (AFR) AF: 0.0351 AC: 1453 AN: 41448

American (AMR) AF: 0.153 AC: 2327 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 616 AN: 3466

East Asian (EAS) AF: 0.0194 AC: 100 AN: 5160

South Asian (SAS) AF: 0.0864 AC: 415 AN: 4802

European-Finnish (FIN) AF: 0.274 AC: 2885 AN: 10538

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.211 AC: 14354 AN: 67948

Other (OTH) AF: 0.169 AC: 356 AN: 2106

Alfa AF: 0.190 Hom.: 10578

Bravo AF: 0.139

Asia WGS AF: 0.0500 AC: 178 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	0.57
DANN	Benign	0.51
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs3118914; hg19: chr13-51116901;