13-50152056-G-C

Variant names:

• chr13-50152056-G-C
• rs1853926
• ENST00000461527.7:n.440+68862G>C

Variant summary

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

The ENST00000461527.7(DLEU1):​n.440+68862G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0265 in 151,032 control chromosomes in the GnomAD database, including 102 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 0.026 (102 hom., cov: 31)
• Consequence: DLEU1 ENST00000461527.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0591 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000461527.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	NR_109974.1		n.442+68862G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000461527.7	TSL:1	n.440+68862G>C		intron	N/A
	DLEU1	ENST00000463474.7	TSL:1	n.440+68862G>C		intron	N/A
	DLEU1	ENST00000468168.6	TSL:1	n.440+68862G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0264 AC: 3989 AN: 150916 Hom.: 101 Cov.: 31

Gnomad AFR AF: 0.0611

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0207

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.000195

Gnomad SAS AF: 0.00461

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0134

Gnomad OTH AF: 0.0252

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

GnomAD4 genome AF: 0.0265 AC: 4000 AN: 151032 Hom.: 102 Cov.: 31 AF XY: 0.0258 AC XY: 1899 AN XY: 73706

African (AFR) AF: 0.0611 AC: 2516 AN: 41168

American (AMR) AF: 0.0208 AC: 314 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3464

East Asian (EAS) AF: 0.000195 AC: 1 AN: 5118

South Asian (SAS) AF: 0.00482 AC: 23 AN: 4770

European-Finnish (FIN) AF: 0.0107 AC: 110 AN: 10294

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0134 AC: 908 AN: 67818

Other (OTH) AF: 0.0249 AC: 52 AN: 2088

Alfa AF: 0.0201 Hom.: 7

Bravo AF: 0.0286

Asia WGS AF: 0.00694 AC: 24 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.38
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1853926; hg19: chr13-50726192;