rs9526689

Variant names:

• chr13-50725131-G-A
• rs9526689
• ENST00000400393.3:c.460-11891C>T

Variant summary

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

The ENST00000400393.3(DLEU7):​c.460-11891C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0564 in 152,082 control chromosomes in the GnomAD database, including 352 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 0.056 (352 hom., cov: 32)
• Consequence: DLEU7 ENST00000400393.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 2 publications found

Genes affected

DLEU7 (HGNC:17567): (deleted in lymphocytic leukemia 7)

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000400393.3. 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
	DLEU7	NM_198989.3		c.460-11891C>T		intron	N/A	NP_945340.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU7	ENST00000400393.3	TSL:1	c.460-11891C>T		intron	N/A	ENSP00000420976.1
	DLEU1	ENST00000650996.1		n.239+9244G>A		intron	N/A
	DLEU7	ENST00000651265.1		n.*469-28553C>T		intron	N/A	ENSP00000516017.1

Frequencies

GnomAD3 genomes AF: 0.0563 AC: 8559 AN: 151964 Hom.: 347 Cov.: 32

Gnomad AFR AF: 0.0136

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0380

Gnomad FIN AF: 0.0760

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0564 AC: 8575 AN: 152082 Hom.: 352 Cov.: 32 AF XY: 0.0571 AC XY: 4248 AN XY: 74344

African (AFR) AF: 0.0136 AC: 564 AN: 41516

American (AMR) AF: 0.116 AC: 1767 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0775 AC: 269 AN: 3470

East Asian (EAS) AF: 0.00194 AC: 10 AN: 5162

South Asian (SAS) AF: 0.0388 AC: 187 AN: 4816

European-Finnish (FIN) AF: 0.0760 AC: 803 AN: 10570

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0713 AC: 4845 AN: 67962

Other (OTH) AF: 0.0488 AC: 103 AN: 2110

Alfa AF: 0.0622 Hom.: 210

Bravo AF: 0.0582

Asia WGS AF: 0.0260 AC: 90 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.76
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9526689; hg19: chr13-51299267;