13-50656996-G-C

Variant names:

• chr13-50656996-G-C
• rs797519
• ENST00000470726.7:n.347-62651G>C

Variant summary

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

The ENST00000651397.1(DLEU7):​n.*571+26910C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,034 control chromosomes in the GnomAD database, including 15,774 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 0.45 (15774 hom., cov: 32)
• Consequence: DLEU7 ENST00000651397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651397.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLEU1	ENST00000470726.7	TSL:5	n.347-62651G>C		intron	N/A
	DLEU7	ENST00000651397.1		n.*571+26910C>G		intron	N/A	ENSP00000516015.1	A0A994J5B2

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67843 AN: 151914 Hom.: 15738 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.447 AC: 67939 AN: 152034 Hom.: 15774 Cov.: 32 AF XY: 0.446 AC XY: 33116 AN XY: 74294

African (AFR) AF: 0.568 AC: 23554 AN: 41458

American (AMR) AF: 0.391 AC: 5969 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1077 AN: 3472

East Asian (EAS) AF: 0.449 AC: 2316 AN: 5160

South Asian (SAS) AF: 0.317 AC: 1529 AN: 4818

European-Finnish (FIN) AF: 0.430 AC: 4546 AN: 10578

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.403 AC: 27416 AN: 67960

Other (OTH) AF: 0.444 AC: 937 AN: 2108

Alfa AF: 0.426 Hom.: 1784

Bravo AF: 0.457

Asia WGS AF: 0.382 AC: 1326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.021
DANN	Benign	0.50
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs797519;

hg19: chr13-51231132;