13-50620269-C-T

Variant names:

• chr13-50620269-C-T
• rs573666
• ENST00000470726.7:n.347-99378C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651397.1(DLEU7):​n.*571+63637G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,004 control chromosomes in the GnomAD database, including 7,379 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 0.30 (7379 hom., cov: 32)
• Consequence: DLEU7 ENST00000651397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837

Genes affected

DLEU1 (HGNC:13747): (deleted in lymphocytic leukemia 1)

DLEU7 (HGNC:17567): (deleted in lymphocytic leukemia 7)

ACMG classification

Verdict is Benign. Variant got -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 = 0.344 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.347-99378C>T		intron_variant	Intron 3 of 5	5
DLEU1	ENST00000479420.5	n.560-28321C>T		intron_variant	Intron 5 of 5	5
DLEU1	ENST00000484869.6	n.1330-11008C>T		intron_variant	Intron 10 of 10	5

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46067 AN: 151886 Hom.: 7379 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.303 AC: 46084 AN: 152004 Hom.: 7379 Cov.: 32 AF XY: 0.304 AC XY: 22569 AN XY: 74288

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.331

Alfa AF: 0.340 Hom.: 18131

Bravo AF: 0.300

Asia WGS AF: 0.226 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs573666; hg19: chr13-51194405;