13-50542765-G-T

Position:

• chr13-50542765-G-T

Variant summary

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

The variant allele was found at a frequency of 0.15 in 151,900 control chromosomes in the GnomAD database, including 2,261 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 (2261 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.616

Genes affected

(HGNC:):

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 = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.50542765G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000470726.7	n.346+109215G>T		intron_variant		5
DLEU1	ENST00000479420.5	n.458-46710G>T		intron_variant		5
DLEU1	ENST00000484869.6	n.1329+39885G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22830 AN: 151780 Hom.: 2262 Cov.: 31

Gnomad AFR AF: 0.0352

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0193

Gnomad SAS AF: 0.0874

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.154

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.150 AC: 22816 AN: 151900 Hom.: 2261 Cov.: 31 AF XY: 0.151 AC XY: 11185 AN XY: 74220

Gnomad4 AFR AF: 0.0351

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.0194

Gnomad4 SAS AF: 0.0864

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.169

Alfa AF: 0.194 Hom.: 4904

Bravo AF: 0.139

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	-0.91
CADD	Benign	0.57
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3118914; hg19: chr13-51116901;