13-50606179-A-G

Variant names:

• chr13-50606179-A-G
• rs797532
• ENST00000469127.6:n.687+16603A>G

Variant summary

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

The ENST00000651397.1(DLEU7):​n.*571+77727T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,988 control chromosomes in the GnomAD database, including 24,484 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 0.56 (24484 hom., cov: 31)
• Consequence: DLEU7 ENST00000651397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• Publications: 7 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 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.687+16603A>G		intron	N/A
	DLEU1	ENST00000470726.7	TSL:5	n.347-113468A>G		intron	N/A
	DLEU1	ENST00000479420.5	TSL:5	n.559+16603A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85030 AN: 151870 Hom.: 24454 Cov.: 31

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.560 AC: 85111 AN: 151988 Hom.: 24484 Cov.: 31 AF XY: 0.557 AC XY: 41376 AN XY: 74274

African (AFR) AF: 0.689 AC: 28573 AN: 41444

American (AMR) AF: 0.503 AC: 7683 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1955 AN: 3468

East Asian (EAS) AF: 0.451 AC: 2331 AN: 5170

South Asian (SAS) AF: 0.608 AC: 2927 AN: 4814

European-Finnish (FIN) AF: 0.470 AC: 4955 AN: 10538

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34973 AN: 67954

Other (OTH) AF: 0.530 AC: 1121 AN: 2114

Alfa AF: 0.540 Hom.: 2799

Bravo AF: 0.561

Asia WGS AF: 0.592 AC: 2055 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.40
DANN	Benign	0.44
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs797532; hg19: chr13-51180315;