rs3116607

Variant names:

• chr13-50547982-C-A
• rs3116607
• ENST00000469127.6:n.586-41493C>A

Your query was ambiguous. Multiple possible variants found:

• chr13-50547982-C-A
• chr13-50547982-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000469127.6(DLEU1):​n.586-41493C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: DLEU1 ENST00000469127.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 7 publications found

Genes affected

DLEU1 (HGNC:13747): (deleted in lymphocytic leukemia 1)

DLEU7 (HGNC:17567): (deleted in lymphocytic leukemia 7)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000469127.6	n.586-41493C>A		intron_variant	Intron 5 of 6	5
DLEU1	ENST00000470726.7	n.346+114432C>A		intron_variant	Intron 3 of 5	5
DLEU1	ENST00000479420.5	n.458-41493C>A		intron_variant	Intron 4 of 5	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

African (AFR) AF: 0.0306 AC: 1269 AN: 41534

American (AMR) AF: 0.130 AC: 1989 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 496 AN: 3470

East Asian (EAS) AF: 0.0141 AC: 73 AN: 5182

South Asian (SAS) AF: 0.0783 AC: 378 AN: 4830

European-Finnish (FIN) AF: 0.269 AC: 2842 AN: 10546

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12409 AN: 67990

Other (OTH) AF: 0.146 AC: 309 AN: 2114

Alfa AF: 0.143 Hom.: 566

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3116607; hg19: chr13-51122118;