chr13-50375812-G-T

Position:

• chr13-50375812-G-T

Variant summary

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

The NR_109974.1(DLEU1):​n.443-14386G>T 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 0.0798 in 151,892 control chromosomes in the GnomAD database, including 541 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 0.080 (541 hom., cov: 29)
• Consequence: DLEU1 NR_109974.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.860

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLEU1	NR_109974.1	n.443-14386G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLEU1	ENST00000490577.5	n.1638-57601G>T		intron_variant, non_coding_transcript_variant		5
	ENST00000652118.1	n.298-1157C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0797 AC: 12102 AN: 151774 Hom.: 534 Cov.: 29

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0659

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.0835

Gnomad FIN AF: 0.0855

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0916

Gnomad OTH AF: 0.0764

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

GnomAD4 genome AF: 0.0798 AC: 12120 AN: 151892 Hom.: 541 Cov.: 29 AF XY: 0.0786 AC XY: 5838 AN XY: 74242

Gnomad4 AFR AF: 0.0700

Gnomad4 AMR AF: 0.0656

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0114

Gnomad4 SAS AF: 0.0836

Gnomad4 FIN AF: 0.0855

Gnomad4 NFE AF: 0.0916

Gnomad4 OTH AF: 0.0856

Alfa AF: 0.0822 Hom.: 499

Bravo AF: 0.0761

Asia WGS AF: 0.0810 AC: 282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12864797; hg19: chr13-50949948;