rs3118912

Positions:

• chr13-50537328-C-T

Variant summary

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

The ENST00000651397.1(DLEU7):​c.*572-11321G>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 0.151 in 152,182 control chromosomes in the GnomAD database, including 2,272 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 0.15 (2272 hom., cov: 32)
• Consequence: DLEU7 ENST00000651397.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389

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=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 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.*572-11321G>A		intron_variant, NMD_transcript_variant
DLEU1	ENST00000470726.7	n.346+103778C>T		intron_variant, non_coding_transcript_variant		5
DLEU1	ENST00000479420.5	n.457+44567C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22954 AN: 152064 Hom.: 2273 Cov.: 32

Gnomad AFR AF: 0.0372

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0194

Gnomad SAS AF: 0.0870

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.151 AC: 22940 AN: 152182 Hom.: 2272 Cov.: 32 AF XY: 0.151 AC XY: 11252 AN XY: 74398

Gnomad4 AFR AF: 0.0371

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.0195

Gnomad4 SAS AF: 0.0860

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.170

Alfa AF: 0.160 Hom.: 413

Bravo AF: 0.140

Asia WGS AF: 0.0500 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.1
DANN	Benign	0.80
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3118912; hg19: chr13-51111464;