rs9526689

chr13-50725131-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLEU7	NM_198989.3	c.460-11891C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLEU7	ENST00000400393.3	c.460-11891C>T		intron_variant		1
DLEU7	ENST00000651265.1	c.*469-28553C>T		intron_variant, NMD_transcript_variant
DLEU7	ENST00000651397.1	c.427-28553C>T		intron_variant, NMD_transcript_variant

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

Gnomad4 AFR AF: 0.0136

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0775

Gnomad4 EAS AF: 0.00194

Gnomad4 SAS AF: 0.0388

Gnomad4 FIN AF: 0.0760

Gnomad4 NFE AF: 0.0713

Gnomad4 OTH AF: 0.0488

Alfa AF: 0.0696 Hom.: 192

Bravo AF: 0.0582

Asia WGS AF: 0.0260 AC: 90 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.1
Dann	Benign	0.76

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

Publications

LitVar

Other links and lift over

dbSNP: rs9526689; hg19: chr13-51299267;