rs1928123

chr13-50545709-A-C

Variant summary

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

The ENST00000651397.1(DLEU7):c.*572-19702T>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,144 control chromosomes in the GnomAD database, including 1,789 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 0.14 (1789 hom., cov: 32)
• Consequence: DLEU7 ENST00000651397.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.209 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.*572-19702T>G		intron_variant, NMD_transcript_variant
DLEU1	ENST00000470726.7	n.346+112159A>C		intron_variant, non_coding_transcript_variant		5
DLEU1	ENST00000479420.5	n.458-43766A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21903 AN: 152026 Hom.: 1775 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.0948

Gnomad EAS AF: 0.0696

Gnomad SAS AF: 0.0959

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.144 AC: 21952 AN: 152144 Hom.: 1789 Cov.: 32 AF XY: 0.146 AC XY: 10870 AN XY: 74364

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.0948

Gnomad4 EAS AF: 0.0688

Gnomad4 SAS AF: 0.0959

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.127

Alfa AF: 0.118 Hom.: 1132

Bravo AF: 0.147

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.4
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1928123; hg19: chr13-51119845;