rs1359612

Variant names:

• chr13-50139945-T-A
• rs1359612
• ENST00000461527.7:n.440+56751T>A

Variant summary

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

The ENST00000461527.7(DLEU1):​n.440+56751T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0391 in 152,334 control chromosomes in the GnomAD database, including 184 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 0.039 (184 hom., cov: 32)
• Consequence: DLEU1 ENST00000461527.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLEU1	NR_109974.1	n.442+56751T>A		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000461527.7	n.440+56751T>A		intron_variant	Intron 2 of 5	1
DLEU1	ENST00000463474.7	n.440+56751T>A		intron_variant	Intron 2 of 5	1
DLEU1	ENST00000468168.5	n.440+56751T>A		intron_variant	Intron 2 of 5	1

Frequencies

GnomAD3 genomes AF: 0.0392 AC: 5965 AN: 152216 Hom.: 184 Cov.: 32

Gnomad AFR AF: 0.00924

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0442

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.000768

Gnomad SAS AF: 0.0122

Gnomad FIN AF: 0.0597

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0538

Gnomad OTH AF: 0.0587

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

GnomAD4 genome AF: 0.0391 AC: 5963 AN: 152334 Hom.: 184 Cov.: 32 AF XY: 0.0384 AC XY: 2859 AN XY: 74490

Gnomad4 AFR AF: 0.00921

Gnomad4 AMR AF: 0.0442

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.000770

Gnomad4 SAS AF: 0.0122

Gnomad4 FIN AF: 0.0597

Gnomad4 NFE AF: 0.0537

Gnomad4 OTH AF: 0.0581

Alfa AF: 0.0463 Hom.: 26

Bravo AF: 0.0376

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1359612; hg19: chr13-50714081;