13-50531198-G-A

Variant names:

• chr13-50531198-G-A
• rs3118905
• ENST00000460525.6:n.363-1995G>A

Variant summary

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

The ENST00000460525.6(DLEU1):​n.363-1995G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 151,508 control chromosomes in the GnomAD database, including 3,940 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 0.21 (3940 hom., cov: 32)
• Consequence: DLEU1 ENST00000460525.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 52 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000460525.6. 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	ENST00000460525.6	TSL:1	n.363-1995G>A		intron	N/A
	DLEU1	ENST00000462427.2	TSL:1	n.452-1995G>A		intron	N/A
	DLEU1	ENST00000469127.6	TSL:5	n.585+25518G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31817 AN: 151390 Hom.: 3940 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.0199

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.210 AC: 31819 AN: 151508 Hom.: 3940 Cov.: 32 AF XY: 0.209 AC XY: 15437 AN XY: 74016

African (AFR) AF: 0.101 AC: 4186 AN: 41406

American (AMR) AF: 0.204 AC: 3102 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3470

East Asian (EAS) AF: 0.0200 AC: 103 AN: 5162

South Asian (SAS) AF: 0.125 AC: 602 AN: 4806

European-Finnish (FIN) AF: 0.333 AC: 3466 AN: 10420

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18535 AN: 67706

Other (OTH) AF: 0.236 AC: 495 AN: 2094

Alfa AF: 0.253 Hom.: 16873

Bravo AF: 0.198

Asia WGS AF: 0.0710 AC: 247 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.87
DANN	Benign	0.73
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3118905; hg19: chr13-51105334;