rs797509

chr13-50708286-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651397.1(DLEU7):c.427-11708G>C variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,996 control chromosomes in the GnomAD database, including 11,586 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 0.35 (11586 hom., cov: 32)
• Consequence: DLEU7 ENST00000651397.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLEU7	ENST00000651265.1	c.*469-11708G>C		intron_variant, NMD_transcript_variant
DLEU7	ENST00000651397.1	c.427-11708G>C		intron_variant, NMD_transcript_variant
DLEU1	ENST00000470726.7	n.347-11361C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52865 AN: 151876 Hom.: 11541 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.349 AC: 52974 AN: 151996 Hom.: 11586 Cov.: 32 AF XY: 0.346 AC XY: 25717 AN XY: 74310

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.301

Alfa AF: 0.298 Hom.: 1063

Bravo AF: 0.364

Asia WGS AF: 0.268 AC: 932 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	0.56
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs797509; hg19: chr13-51282422;