rs7991818

chr13-50636244-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+47662G>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 0.163 in 151,986 control chromosomes in the GnomAD database, including 2,559 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 0.16 (2559 hom., cov: 31)
• Consequence: DLEU7 ENST00000651397.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 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+47662G>A		intron_variant, NMD_transcript_variant
DLEU1	ENST00000470726.7	n.347-83403C>T		intron_variant, non_coding_transcript_variant		5
DLEU1	ENST00000479420.5	n.560-12346C>T		intron_variant, non_coding_transcript_variant		5
DLEU1	ENST00000647700.1	n.883-12349C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24709 AN: 151868 Hom.: 2555 Cov.: 31

Gnomad AFR AF: 0.0431

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.0718

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.163 AC: 24718 AN: 151986 Hom.: 2559 Cov.: 31 AF XY: 0.164 AC XY: 12156 AN XY: 74266

Gnomad4 AFR AF: 0.0433

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.0708

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.183

Alfa AF: 0.213 Hom.: 7251

Bravo AF: 0.153

Asia WGS AF: 0.0750 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.3
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7991818; hg19: chr13-51210380;