chr13-50361786-C-T

Variant names:

• chr13-50361786-C-T
• rs12874278
• ENST00000461527.7:n.556-53303C>T

Variant summary

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

The ENST00000461527.7(DLEU1):​n.556-53303C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0623 in 472,988 control chromosomes in the GnomAD database, including 1,053 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 0.064 (365 hom., cov: 32)
  • Exomes 𝑓: 0.061 (688 hom.)
• Consequence: DLEU1 ENST00000461527.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 7 publications found

Genes affected

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

RPL34P26 (HGNC:36100): (ribosomal protein L34 pseudogene 26)

ENSG00000286191 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0747 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000461527.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	NR_109974.1		n.443-28412C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000461527.7	TSL:1	n.556-53303C>T		intron	N/A
	DLEU1	ENST00000463357.5	TSL:1	n.181-28412C>T		intron	N/A
	DLEU1	ENST00000463474.7	TSL:1	n.599+22952C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0643 AC: 9779 AN: 152058 Hom.: 358 Cov.: 32

Gnomad AFR AF: 0.0769

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0539

Gnomad ASJ AF: 0.0674

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.0742

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0663

Gnomad OTH AF: 0.0603

GnomAD4 exome AF: 0.0613 AC: 19673 AN: 320812 Hom.: 688 Cov.: 0 AF XY: 0.0635 AC XY: 11542 AN XY: 181858

African (AFR) AF: 0.0810 AC: 732 AN: 9040

American (AMR) AF: 0.0416 AC: 1080 AN: 25962

Ashkenazi Jewish (ASJ) AF: 0.0587 AC: 515 AN: 8768

East Asian (EAS) AF: 0.0110 AC: 170 AN: 15448

South Asian (SAS) AF: 0.0760 AC: 4216 AN: 55468

European-Finnish (FIN) AF: 0.0412 AC: 588 AN: 14288

Middle Eastern (MID) AF: 0.0572 AC: 63 AN: 1102

European-Non Finnish (NFE) AF: 0.0647 AC: 11341 AN: 175316

Other (OTH) AF: 0.0628 AC: 968 AN: 15420

GnomAD4 genome AF: 0.0644 AC: 9805 AN: 152176 Hom.: 365 Cov.: 32 AF XY: 0.0633 AC XY: 4711 AN XY: 74404

African (AFR) AF: 0.0769 AC: 3194 AN: 41512

American (AMR) AF: 0.0536 AC: 820 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0674 AC: 234 AN: 3470

East Asian (EAS) AF: 0.0114 AC: 59 AN: 5188

South Asian (SAS) AF: 0.0742 AC: 358 AN: 4822

European-Finnish (FIN) AF: 0.0414 AC: 438 AN: 10588

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0662 AC: 4504 AN: 67988

Other (OTH) AF: 0.0691 AC: 146 AN: 2112

Alfa AF: 0.0634 Hom.: 541

Bravo AF: 0.0641

Asia WGS AF: 0.0790 AC: 275 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	2.4
DANN	Benign	0.58
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs12874278; hg19: chr13-50935922;