rs3116607

Positions:

• chr13-50547982-C-A
• chr13-50547982-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 0.132 in 152,140 control chromosomes in the GnomAD database, including 1,784 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 0.13 (1784 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.50547982C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000470726.7	n.346+114432C>A		intron_variant		5
DLEU1	ENST00000479420.5	n.458-41493C>A		intron_variant		5
DLEU1	ENST00000484869.6	n.1329+45102C>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20066 AN: 152022 Hom.: 1785 Cov.: 32

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.0792

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.132 AC: 20053 AN: 152140 Hom.: 1784 Cov.: 32 AF XY: 0.134 AC XY: 9930 AN XY: 74352

Gnomad4 AFR AF: 0.0306

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.0141

Gnomad4 SAS AF: 0.0783

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.146

Alfa AF: 0.108 Hom.: 200

Bravo AF: 0.120

Asia WGS AF: 0.0470 AC: 168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.50
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3116607; hg19: chr13-51122118;