rs3118916

Variant names:

• chr13-50562672-G-A
• rs3118916
• ENST00000470726.7:n.346+129122G>A

Variant summary

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

The ENST00000651397.1(DLEU7):​n.*572-36665C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,010 control chromosomes in the GnomAD database, including 2,195 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 (2195 hom., cov: 31)
• Consequence: DLEU7 ENST00000651397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000470726.7	n.346+129122G>A		intron_variant	Intron 3 of 5	5
DLEU1	ENST00000479420.5	n.458-26803G>A		intron_variant	Intron 4 of 5	5
DLEU1	ENST00000484869.6	n.1329+59792G>A		intron_variant	Intron 10 of 10	5

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22452 AN: 151892 Hom.: 2196 Cov.: 31

Gnomad AFR AF: 0.0368

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.0862

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.148 AC: 22439 AN: 152010 Hom.: 2195 Cov.: 31 AF XY: 0.148 AC XY: 11002 AN XY: 74296

Gnomad4 AFR AF: 0.0366

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.0211

Gnomad4 SAS AF: 0.0853

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.168

Alfa AF: 0.182 Hom.: 1369

Bravo AF: 0.137

Asia WGS AF: 0.0520 AC: 185 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	5.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3118916; hg19: chr13-51136808;