rs790531

Positions:

• chr13-50151378-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109974.1(DLEU1):​n.442+68184A>G 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 0.107 in 152,160 control chromosomes in the GnomAD database, including 1,194 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 0.11 (1194 hom., cov: 32)
• Consequence: DLEU1 NR_109974.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLEU1	NR_109974.1	n.442+68184A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000490577.5	n.388-5449A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16183 AN: 152042 Hom.: 1186 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0846

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.0826

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0592

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0599

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.107 AC: 16216 AN: 152160 Hom.: 1194 Cov.: 32 AF XY: 0.107 AC XY: 7984 AN XY: 74418

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.0845

Gnomad4 ASJ AF: 0.0591

Gnomad4 EAS AF: 0.0824

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.0592

Gnomad4 NFE AF: 0.0600

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0758 Hom.: 309

Bravo AF: 0.112

Asia WGS AF: 0.153 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs790531; hg19: chr13-50725514;