rs536338

Positions:

• chr13-50529325-C-G
• chr13-50529325-C-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 0.746 in 152,110 control chromosomes in the GnomAD database, including 42,506 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 0.75 (42506 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

Genes affected

DLEU1 (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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.50529325C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000460525.6	n.363-3868C>G		intron_variant		1
DLEU1	ENST00000462427.2	n.451+1261C>G		intron_variant		1
DLEU1	ENST00000470726.7	n.346+95775C>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113457 AN: 151992 Hom.: 42476 Cov.: 31

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.746 AC: 113538 AN: 152110 Hom.: 42506 Cov.: 31 AF XY: 0.745 AC XY: 55395 AN XY: 74338

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.799

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.723

Alfa AF: 0.732 Hom.: 5065

Bravo AF: 0.753

Asia WGS AF: 0.705 AC: 2453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs536338; hg19: chr13-51103461;