rs723801

Positions:

• chr13-50259271-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.443-130927A>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 0.155 in 151,050 control chromosomes in the GnomAD database, including 2,098 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 0.15 (2098 hom., cov: 31)
• Consequence: DLEU1 NR_109974.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366

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 (AMR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLEU1	NR_109974.1	n.443-130927A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLEU1	ENST00000490577.5	n.1637+101195A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23360 AN: 150936 Hom.: 2091 Cov.: 31

Gnomad AFR AF: 0.0859

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0254

Gnomad SAS AF: 0.0942

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.155 AC: 23386 AN: 151050 Hom.: 2098 Cov.: 31 AF XY: 0.156 AC XY: 11485 AN XY: 73740

Gnomad4 AFR AF: 0.0859

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.0251

Gnomad4 SAS AF: 0.0945

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.165

Alfa AF: 0.177 Hom.: 456

Bravo AF: 0.154

Asia WGS AF: 0.0740 AC: 256 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.70
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs723801; hg19: chr13-50833407;