rs17074558

Variant names:

• chr13-50544313-G-A
• rs17074558
• ENST00000469127.6:n.585+38633G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000651397.1(DLEU7):​n.*572-18306C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0695 in 152,106 control chromosomes in the GnomAD database, including 432 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 0.069 (432 hom., cov: 32)
• Consequence: DLEU7 ENST00000651397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70
• Publications: 1 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0852 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+38633G>A		intron	N/A
	DLEU1	ENST00000470726.7	TSL:5	n.346+110763G>A		intron	N/A
	DLEU1	ENST00000479420.5	TSL:5	n.458-45162G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0694 AC: 10548 AN: 151986 Hom.: 431 Cov.: 32

Gnomad AFR AF: 0.0574

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0498

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.0914

Gnomad FIN AF: 0.0701

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0826

Gnomad OTH AF: 0.0737

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

GnomAD4 genome AF: 0.0695 AC: 10565 AN: 152106 Hom.: 432 Cov.: 32 AF XY: 0.0689 AC XY: 5124 AN XY: 74352

African (AFR) AF: 0.0572 AC: 2372 AN: 41492

American (AMR) AF: 0.0498 AC: 760 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0956 AC: 332 AN: 3472

East Asian (EAS) AF: 0.0191 AC: 99 AN: 5182

South Asian (SAS) AF: 0.0923 AC: 444 AN: 4810

European-Finnish (FIN) AF: 0.0701 AC: 741 AN: 10570

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0826 AC: 5616 AN: 67988

Other (OTH) AF: 0.0799 AC: 169 AN: 2114

Alfa AF: 0.0820 Hom.: 456

Bravo AF: 0.0663

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	14
DANN	Benign	0.77
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs17074558; hg19: chr13-51118449;