rs797523

Positions:

• chr13-50601892-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000651397.1(DLEU7):​n.*572-75885C>T 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: DLEU7 ENST00000651397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 3698 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000470726.7	n.347-117755G>A		intron_variant		5
DLEU1	ENST00000479420.5	n.559+12316G>A		intron_variant		5
DLEU1	ENST00000484869.6	n.1330-29385G>A		intron_variant		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

Gnomad4 AFR AF: 0.0384

Gnomad4 AMR AF: 0.0174

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.00967

Gnomad4 SAS AF: 0.0178

Gnomad4 FIN AF: 0.0135

Gnomad4 NFE AF: 0.0198

Gnomad4 OTH AF: 0.0208

Alfa AF: 0.0206 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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs797523; hg19: chr13-51176028;