rs12874278

Positions:

• chr13-50361786-C-T

Variant summary

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

The NR_109974.1(DLEU1):​n.443-28412C>T variant causes a intron, non coding transcript 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 NR_109974.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLEU1	NR_109974.1	n.443-28412C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLEU1	ENST00000490577.5	n.1638-71627C>T		intron_variant, non_coding_transcript_variant		5
RPL34P26	ENST00000445636.1			upstream_gene_variant

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

Gnomad4 AFR exome AF: 0.0810

Gnomad4 AMR exome AF: 0.0416

Gnomad4 ASJ exome AF: 0.0587

Gnomad4 EAS exome AF: 0.0110

Gnomad4 SAS exome AF: 0.0760

Gnomad4 FIN exome AF: 0.0412

Gnomad4 NFE exome AF: 0.0647

Gnomad4 OTH exome AF: 0.0628

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

Gnomad4 AFR AF: 0.0769

Gnomad4 AMR AF: 0.0536

Gnomad4 ASJ AF: 0.0674

Gnomad4 EAS AF: 0.0114

Gnomad4 SAS AF: 0.0742

Gnomad4 FIN AF: 0.0414

Gnomad4 NFE AF: 0.0662

Gnomad4 OTH AF: 0.0691

Alfa AF: 0.0639 Hom.: 416

Bravo AF: 0.0641

Asia WGS AF: 0.0790 AC: 275 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12874278; hg19: chr13-50935922;