rs536338

Variant names:

• chr13-50529325-C-G
• rs536338
• ENST00000468168.6:n.2243C>G

Your query was ambiguous. Multiple possible variants found:

• chr13-50529325-C-G
• chr13-50529325-C-T

Variant summary

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

The ENST00000468168.6(DLEU1):​n.2243C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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: DLEU1 ENST00000468168.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480
• Publications: 4 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000468168.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000468168.6	TSL:1	n.2243C>G		non_coding_transcript_exon	Exon 6 of 6
	DLEU1	ENST00000460525.6	TSL:1	n.363-3868C>G		intron	N/A
	DLEU1	ENST00000462427.2	TSL:1	n.451+1261C>G		intron	N/A

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

African (AFR) AF: 0.770 AC: 31961 AN: 41498

American (AMR) AF: 0.799 AC: 12211 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2491 AN: 3466

East Asian (EAS) AF: 0.848 AC: 4369 AN: 5154

South Asian (SAS) AF: 0.613 AC: 2958 AN: 4822

European-Finnish (FIN) AF: 0.772 AC: 8170 AN: 10580

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48933 AN: 67986

Other (OTH) AF: 0.723 AC: 1526 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.75
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs536338; hg19: chr13-51103461;