rs3095160

Positions:

• chr13-50372132-A-G

Variant summary

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

The ENST00000461527.7(DLEU1):​n.556-42957A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,116 control chromosomes in the GnomAD database, including 2,655 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 0.18 (2655 hom., cov: 32)
• Consequence: DLEU1 ENST00000461527.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.900

Genes affected

DLEU1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DLEU1	NR_109974.1	n.443-18066A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DLEU1	ENST00000461527.7	n.556-42957A>G		intron_variant		1
DLEU1	ENST00000463357.5	n.181-18066A>G		intron_variant		1
DLEU1	ENST00000463474.7	n.599+33298A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27420 AN: 151998 Hom.: 2641 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.0265

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.180 AC: 27453 AN: 152116 Hom.: 2655 Cov.: 32 AF XY: 0.174 AC XY: 12937 AN XY: 74362

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.0268

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.182

Alfa AF: 0.182 Hom.: 540

Bravo AF: 0.181

Asia WGS AF: 0.156 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	15
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3095160; hg19: chr13-50946268;