rs3116605

Variant names:

• chr13-50543426-T-C
• rs3116605
• ENST00000469127.6:n.585+37746T>C

Variant summary

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

The ENST00000651397.1(DLEU7):​n.*572-17419A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 149,726 control chromosomes in the GnomAD database, including 2,274 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 (2274 hom., cov: 31)
• Consequence: DLEU7 ENST00000651397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 9 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 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+37746T>C		intron	N/A
	DLEU1	ENST00000470726.7	TSL:5	n.346+109876T>C		intron	N/A
	DLEU1	ENST00000479420.5	TSL:5	n.458-46049T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.154 AC: 22968 AN: 149604 Hom.: 2275 Cov.: 31

Gnomad AFR AF: 0.0390

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.0897

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.153 AC: 22955 AN: 149726 Hom.: 2274 Cov.: 31 AF XY: 0.154 AC XY: 11252 AN XY: 72992

African (AFR) AF: 0.0389 AC: 1563 AN: 40210

American (AMR) AF: 0.157 AC: 2341 AN: 14930

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 615 AN: 3454

East Asian (EAS) AF: 0.0198 AC: 100 AN: 5038

South Asian (SAS) AF: 0.0888 AC: 415 AN: 4676

European-Finnish (FIN) AF: 0.277 AC: 2880 AN: 10384

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14368 AN: 67758

Other (OTH) AF: 0.174 AC: 361 AN: 2076

Alfa AF: 0.190 Hom.: 5282

Bravo AF: 0.140

Asia WGS AF: 0.0510 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.5
DANN	Benign	0.68
PhyloP100		0.089

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: rs3116605;

hg19: chr13-51117562;