13-50545709-A-C

Variant names:

• chr13-50545709-A-C
• rs1928123
• ENST00000469127.6:n.585+40029A>C

Variant summary

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

The ENST00000469127.6(DLEU1):​n.585+40029A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,144 control chromosomes in the GnomAD database, including 1,789 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 0.14 (1789 hom., cov: 32)
• Consequence: DLEU1 ENST00000469127.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000469127.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000469127.6	TSL:5	n.585+40029A>C		intron	N/A
	DLEU1	ENST00000470726.7	TSL:5	n.346+112159A>C		intron	N/A
	DLEU1	ENST00000479420.5	TSL:5	n.458-43766A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21903 AN: 152026 Hom.: 1775 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.0948

Gnomad EAS AF: 0.0696

Gnomad SAS AF: 0.0959

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.144 AC: 21952 AN: 152144 Hom.: 1789 Cov.: 32 AF XY: 0.146 AC XY: 10870 AN XY: 74364

African (AFR) AF: 0.156 AC: 6476 AN: 41498

American (AMR) AF: 0.215 AC: 3284 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0948 AC: 329 AN: 3472

East Asian (EAS) AF: 0.0688 AC: 356 AN: 5176

South Asian (SAS) AF: 0.0959 AC: 463 AN: 4826

European-Finnish (FIN) AF: 0.213 AC: 2256 AN: 10584

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8463 AN: 67986

Other (OTH) AF: 0.127 AC: 269 AN: 2114

Alfa AF: 0.123 Hom.: 1577

Bravo AF: 0.147

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.69
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs1928123; hg19: chr13-51119845;