rs201762

chr13-50491700-T-G

Variant summary

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

The NR_109974.1(DLEU1):n.675-951T>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 0.161 in 152,210 control chromosomes in the GnomAD database, including 2,475 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 0.16 (2475 hom., cov: 32)
• Consequence: DLEU1 NR_109974.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLEU1	NR_109974.1	n.675-951T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLEU1	ENST00000490577.5	n.1776-951T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24541 AN: 152092 Hom.: 2476 Cov.: 32

Gnomad AFR AF: 0.0541

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.0204

Gnomad SAS AF: 0.0933

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.161 AC: 24534 AN: 152210 Hom.: 2475 Cov.: 32 AF XY: 0.161 AC XY: 11941 AN XY: 74394

Gnomad4 AFR AF: 0.0540

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.0202

Gnomad4 SAS AF: 0.0925

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.180

Alfa AF: 0.198 Hom.: 1722

Bravo AF: 0.151

Asia WGS AF: 0.0600 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.7
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs201762; hg19: chr13-51065836;