rs797523

Variant names:

• chr13-50601892-G-A
• rs797523
• ENST00000469127.6:n.687+12316G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000469127.6(DLEU1):​n.687+12316G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0243 in 152,046 control chromosomes in the GnomAD database, including 48 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 0.024 (48 hom., cov: 32)
• Consequence: DLEU1 ENST00000469127.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 3 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0243 (3698/152046) while in subpopulation AFR AF = 0.0384 (1593/41486). AF 95% confidence interval is 0.0368. There are 48 homozygotes in GnomAd4. There are 1826 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 48 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000469127.6	n.687+12316G>A		intron_variant	Intron 6 of 6	5
DLEU1	ENST00000470726.7	n.347-117755G>A		intron_variant	Intron 3 of 5	5
DLEU1	ENST00000479420.5	n.559+12316G>A		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.0243 AC: 3696 AN: 151928 Hom.: 48 Cov.: 32

Gnomad AFR AF: 0.0385

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0175

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.00965

Gnomad SAS AF: 0.0176

Gnomad FIN AF: 0.0135

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0198

Gnomad OTH AF: 0.0215

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

GnomAD4 genome AF: 0.0243 AC: 3698 AN: 152046 Hom.: 48 Cov.: 32 AF XY: 0.0246 AC XY: 1826 AN XY: 74318

African (AFR) AF: 0.0384 AC: 1593 AN: 41486

American (AMR) AF: 0.0174 AC: 266 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3470

East Asian (EAS) AF: 0.00967 AC: 50 AN: 5170

South Asian (SAS) AF: 0.0178 AC: 86 AN: 4818

European-Finnish (FIN) AF: 0.0135 AC: 142 AN: 10552

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0198 AC: 1344 AN: 67966

Other (OTH) AF: 0.0208 AC: 44 AN: 2112

Alfa AF: 0.0215 Hom.: 7

Bravo AF: 0.0251

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.019
DANN	Benign	0.40
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs797523; hg19: chr13-51176028;