chr13-50708286-C-G

Variant names:

• chr13-50708286-C-G
• rs797509
• ENST00000470726.7:n.347-11361C>G

Variant summary

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

The ENST00000470726.7(DLEU1):​n.347-11361C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,996 control chromosomes in the GnomAD database, including 11,586 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 0.35 (11586 hom., cov: 32)
• Consequence: DLEU1 ENST00000470726.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000470726.7	n.347-11361C>G		intron_variant	Intron 3 of 5	5
DLEU1	ENST00000650910.1	n.386-4252C>G		intron_variant	Intron 1 of 3
DLEU7	ENST00000651265.1	n.*469-11708G>C		intron_variant	Intron 3 of 3			ENSP00000516017.1

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52865 AN: 151876 Hom.: 11541 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.349 AC: 52974 AN: 151996 Hom.: 11586 Cov.: 32 AF XY: 0.346 AC XY: 25717 AN XY: 74310

African (AFR) AF: 0.629 AC: 26085 AN: 41446

American (AMR) AF: 0.280 AC: 4278 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 755 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1050 AN: 5152

South Asian (SAS) AF: 0.197 AC: 950 AN: 4820

European-Finnish (FIN) AF: 0.280 AC: 2956 AN: 10572

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15989 AN: 67958

Other (OTH) AF: 0.301 AC: 633 AN: 2100

Alfa AF: 0.298 Hom.: 1063

Bravo AF: 0.364

Asia WGS AF: 0.268 AC: 932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.51
PhyloP100		-0.056

Splicing

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

Other links and lift over

dbSNP: rs797509; hg19: chr13-51282422;