rs3118906

Positions:

• chr13-50532652-G-A

Variant summary

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

The ENST00000651397.1(DLEU7):​c.*572-6645C>T variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 151,838 control chromosomes in the GnomAD database, including 3,947 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 0.21 (3947 hom., cov: 32)
• Consequence: DLEU7 ENST00000651397.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

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	ENST00000460525.6	n.363-541G>A		intron_variant, non_coding_transcript_variant		1
DLEU1	ENST00000462427.2	n.452-541G>A		intron_variant, non_coding_transcript_variant		1
DLEU7	ENST00000651397.1	c.*572-6645C>T		intron_variant, NMD_transcript_variant				ENSP00000516015

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31844 AN: 151718 Hom.: 3947 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.0197

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.210 AC: 31846 AN: 151838 Hom.: 3947 Cov.: 32 AF XY: 0.208 AC XY: 15456 AN XY: 74240

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.0197

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.234

Alfa AF: 0.265 Hom.: 7281

Bravo AF: 0.198

Asia WGS AF: 0.0720 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3118906; hg19: chr13-51106788;