rs573666

chr13-50620269-C-T

Variant summary

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

The ENST00000651397.1(DLEU7):c.*571+63637G>A variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,004 control chromosomes in the GnomAD database, including 7,379 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 0.30 (7379 hom., cov: 32)
• Consequence: DLEU7 ENST00000651397.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 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	ENST00000651397.1	c.*571+63637G>A		intron_variant, NMD_transcript_variant
DLEU1	ENST00000470726.7	n.347-99378C>T		intron_variant, non_coding_transcript_variant		5
DLEU1	ENST00000479420.5	n.560-28321C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46067 AN: 151886 Hom.: 7379 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.303 AC: 46084 AN: 152004 Hom.: 7379 Cov.: 32 AF XY: 0.304 AC XY: 22569 AN XY: 74288

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.331

Alfa AF: 0.340 Hom.: 18131

Bravo AF: 0.300

Asia WGS AF: 0.226 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.12
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs573666; hg19: chr13-51194405;