rs9316505

Variant names:

• chr13-50816462-G-A
• rs9316505
• ENST00000400393.3:c.459+26726C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-50816462-G-A
• chr13-50816462-G-C

Variant summary

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

The ENST00000400393.3(DLEU7):​c.459+26726C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,936 control chromosomes in the GnomAD database, including 29,451 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 0.61 (29451 hom., cov: 31)
• Consequence: DLEU7 ENST00000400393.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.79
• Publications: 11 publications found

Genes affected

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

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

DLEU7-AS1 (HGNC:39966): (DLEU7 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLEU7	NM_198989.3	c.459+26726C>T		intron_variant	Intron 1 of 1		NP_945340.2
DLEU7-AS1	NR_046551.1	n.300-2059G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLEU7	ENST00000400393.3	c.459+26726C>T		intron_variant	Intron 1 of 1	1		ENSP00000420976.1
DLEU1	ENST00000413510.4	n.300-2059G>A		intron_variant	Intron 2 of 4	1
DLEU1	ENST00000650996.1	n.530-2059G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93299 AN: 151818 Hom.: 29410 Cov.: 31

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.615 AC: 93383 AN: 151936 Hom.: 29451 Cov.: 31 AF XY: 0.610 AC XY: 45243 AN XY: 74226

African (AFR) AF: 0.765 AC: 31754 AN: 41486

American (AMR) AF: 0.549 AC: 8374 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2007 AN: 3464

East Asian (EAS) AF: 0.454 AC: 2322 AN: 5120

South Asian (SAS) AF: 0.401 AC: 1933 AN: 4818

European-Finnish (FIN) AF: 0.582 AC: 6128 AN: 10536

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.574 AC: 38982 AN: 67936

Other (OTH) AF: 0.610 AC: 1290 AN: 2116

Alfa AF: 0.579 Hom.: 52576

Bravo AF: 0.620

Asia WGS AF: 0.430 AC: 1498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	13
DANN	Benign	0.76
PhyloP100		1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9316505; hg19: chr13-51390598;