rs723801

Variant names:

• chr13-50259271-A-G
• rs723801
• ENST00000461527.7:n.441-15661A>G

Variant summary

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

The ENST00000461527.7(DLEU1):​n.441-15661A>G variant causes a intron 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 ENST00000461527.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DLEU1	NR_109974.1	n.443-130927A>G		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000461527.7	n.441-15661A>G		intron_variant	Intron 2 of 5	1
DLEU1	ENST00000463474.7	n.441-79405A>G		intron_variant	Intron 2 of 5	1
DLEU1	ENST00000468168.6	n.441-130927A>G		intron_variant	Intron 2 of 5	1

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

African (AFR) AF: 0.0859 AC: 3535 AN: 41152

American (AMR) AF: 0.228 AC: 3462 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3470

East Asian (EAS) AF: 0.0251 AC: 129 AN: 5142

South Asian (SAS) AF: 0.0945 AC: 452 AN: 4782

European-Finnish (FIN) AF: 0.213 AC: 2174 AN: 10204

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.184 AC: 12453 AN: 67828

Other (OTH) AF: 0.165 AC: 345 AN: 2092

Alfa AF: 0.176 Hom.: 491

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
PhyloP100		0.37
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

Other links and lift over

dbSNP: rs723801; hg19: chr13-50833407;