rs3118916

Variant names:

• chr13-50562672-G-A
• rs3118916
• ENST00000469127.6:n.586-26803G>A

Variant summary

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

The ENST00000469127.6(DLEU1):​n.586-26803G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,010 control chromosomes in the GnomAD database, including 2,195 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 (2195 hom., cov: 31)
• Consequence: DLEU1 ENST00000469127.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• Publications: 10 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 = 0.203 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000469127.6	TSL:5	n.586-26803G>A		intron	N/A
	DLEU1	ENST00000470726.7	TSL:5	n.346+129122G>A		intron	N/A
	DLEU1	ENST00000479420.5	TSL:5	n.458-26803G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22452 AN: 151892 Hom.: 2196 Cov.: 31

Gnomad AFR AF: 0.0368

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.0862

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.148 AC: 22439 AN: 152010 Hom.: 2195 Cov.: 31 AF XY: 0.148 AC XY: 11002 AN XY: 74296

African (AFR) AF: 0.0366 AC: 1520 AN: 41476

American (AMR) AF: 0.146 AC: 2223 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 654 AN: 3472

East Asian (EAS) AF: 0.0211 AC: 109 AN: 5178

South Asian (SAS) AF: 0.0853 AC: 411 AN: 4820

European-Finnish (FIN) AF: 0.273 AC: 2876 AN: 10532

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13978 AN: 67944

Other (OTH) AF: 0.168 AC: 354 AN: 2106

Alfa AF: 0.183 Hom.: 4935

Bravo AF: 0.137

Asia WGS AF: 0.0520 AC: 185 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	5.0
DANN	Benign	0.62
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs3118916; hg19: chr13-51136808;