rs1454626

Variant names:

• chr9-2621030-C-A
• rs1454626
• ENST00000453601.5:n.274+1070G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-2621030-C-A
• chr9-2621030-C-G
• chr9-2621030-C-T

Variant summary

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

The ENST00000453601.5(VLDLR-AS1):​n.274+1070G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 152,072 control chromosomes in the GnomAD database, including 33,678 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 0.66 (33678 hom., cov: 32)
• Consequence: VLDLR-AS1 ENST00000453601.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578

Genes affected

VLDLR-AS1 (HGNC:49621): (VLDLR antisense RNA 1)

VLDLR (HGNC:12698): (very low density lipoprotein receptor) The low density lipoprotein receptor (LDLR) gene family consists of cell surface proteins involved in receptor-mediated endocytosis of specific ligands. This gene encodes a lipoprotein receptor that is a member of the LDLR family and plays important roles in VLDL-triglyceride metabolism and the reelin signaling pathway. Mutations in this gene cause VLDLR-associated cerebellar hypoplasia. Alternative splicing generates multiple transcript variants encoding distinct isoforms for this gene. [provided by RefSeq, Aug 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VLDLR-AS1	NR_015375.2	n.274+1070G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VLDLR-AS1	ENST00000453601.5	n.274+1070G>T		intron_variant	Intron 1 of 3	1
VLDLR-AS1	ENST00000416826.6	n.185+199G>T		intron_variant	Intron 1 of 10	2
VLDLR-AS1	ENST00000447278.2	n.158+199G>T		intron_variant	Intron 1 of 9	3

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100203 AN: 151952 Hom.: 33657 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.659 AC: 100254 AN: 152072 Hom.: 33678 Cov.: 32 AF XY: 0.660 AC XY: 49106 AN XY: 74352

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.653

Alfa AF: 0.693 Hom.: 45710

Bravo AF: 0.657

Asia WGS AF: 0.685 AC: 2384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1454626; hg19: chr9-2621030;