rs3118650

Positions:

• chr13-50455188-A-G

Variant summary

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

The NR_109974.1(DLEU1):​n.674+21638A>G 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 0.0767 in 150,790 control chromosomes in the GnomAD database, including 487 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 0.077 (487 hom., cov: 32)
• Consequence: DLEU1 NR_109974.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLEU1	NR_109974.1	n.674+21638A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLEU1	ENST00000490577.5	n.1775+21638A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0766 AC: 11544 AN: 150674 Hom.: 480 Cov.: 32

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.0640

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0884

Gnomad FIN AF: 0.0490

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0895

Gnomad OTH AF: 0.0861

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

GnomAD4 genome AF: 0.0767 AC: 11561 AN: 150790 Hom.: 487 Cov.: 32 AF XY: 0.0746 AC XY: 5491 AN XY: 73636

Gnomad4 AFR AF: 0.0695

Gnomad4 AMR AF: 0.0638

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.0140

Gnomad4 SAS AF: 0.0883

Gnomad4 FIN AF: 0.0490

Gnomad4 NFE AF: 0.0894

Gnomad4 OTH AF: 0.0952

Alfa AF: 0.0866 Hom.: 308

Bravo AF: 0.0755

Asia WGS AF: 0.0790 AC: 275 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	0.49
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3118650; hg19: chr13-51029324;