rs9596270

Positions:

• chr13-50268304-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_109974.1(DLEU1):​n.443-121894T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0597 in 152,274 control chromosomes in the GnomAD database, including 307 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 0.060 (307 hom., cov: 32)
• Consequence: DLEU1 NR_109974.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.766

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLEU1	NR_109974.1	n.443-121894T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLEU1	ENST00000490577.5	n.1637+110228T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0597 AC: 9091 AN: 152160 Hom.: 306 Cov.: 32

Gnomad AFR AF: 0.0432

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.0471

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.000768

Gnomad SAS AF: 0.0410

Gnomad FIN AF: 0.0570

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0746

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0597 AC: 9095 AN: 152274 Hom.: 307 Cov.: 32 AF XY: 0.0583 AC XY: 4344 AN XY: 74486

Gnomad4 AFR AF: 0.0433

Gnomad4 AMR AF: 0.0469

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.000770

Gnomad4 SAS AF: 0.0413

Gnomad4 FIN AF: 0.0570

Gnomad4 NFE AF: 0.0746

Gnomad4 OTH AF: 0.0553

Alfa AF: 0.0712 Hom.: 368

Bravo AF: 0.0576

Asia WGS AF: 0.0230 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	12
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9596270; hg19: chr13-50842440;