rs9316505

chr13-50816462-G-Achr13-50816462-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

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

DLEU7-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
DLEU7-AS1	NR_046551.1	n.300-2059G>A		intron_variant, non_coding_transcript_variant
DLEU7	NM_198989.3	c.459+26726C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLEU7	ENST00000400393.3	c.459+26726C>T		intron_variant		1
DLEU1	ENST00000413510.4	n.300-2059G>A		intron_variant, non_coding_transcript_variant		1
DLEU7	ENST00000651265.1	c.*468+6731C>T		intron_variant, NMD_transcript_variant

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

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.610

Alfa AF: 0.572 Hom.: 35964

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs9316505; hg19: chr13-51390598;