rs9596270

Variant names:

• chr13-50268304-T-C
• rs9596270
• ENST00000461527.7:n.441-6628T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000461527.7(DLEU1):​n.441-6628T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0597 in 152,274 control chromosomes in the GnomAD database, including 307 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 0.060 (307 hom., cov: 32)
• Consequence: DLEU1 ENST00000461527.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.766
• Publications: 21 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0728 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	NR_109974.1		n.443-121894T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000461527.7	TSL:1	n.441-6628T>C		intron	N/A
	DLEU1	ENST00000463474.7	TSL:1	n.441-70372T>C		intron	N/A
	DLEU1	ENST00000468168.6	TSL:1	n.441-121894T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0597 AC: 9091 AN: 152160 Hom.: 306 Cov.: 32

Gnomad AFR AF: 0.0432

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.0471

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.000768

Gnomad SAS AF: 0.0410

Gnomad FIN AF: 0.0570

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0746

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0597 AC: 9095 AN: 152274 Hom.: 307 Cov.: 32 AF XY: 0.0583 AC XY: 4344 AN XY: 74486

African (AFR) AF: 0.0433 AC: 1800 AN: 41560

American (AMR) AF: 0.0469 AC: 718 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 394 AN: 3470

East Asian (EAS) AF: 0.000770 AC: 4 AN: 5194

South Asian (SAS) AF: 0.0413 AC: 199 AN: 4822

European-Finnish (FIN) AF: 0.0570 AC: 605 AN: 10622

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0746 AC: 5069 AN: 67990

Other (OTH) AF: 0.0553 AC: 117 AN: 2116

Alfa AF: 0.0677 Hom.: 616

Bravo AF: 0.0576

Asia WGS AF: 0.0230 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	12
DANN	Benign	0.70
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs9596270; hg19: chr13-50842440;