9-2537815-C-T

Position:

• chr9-2537815-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.429-1362G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,190 control chromosomes in the GnomAD database, including 52,465 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 0.83 (52465 hom., cov: 32)
• Consequence: VLDLR-AS1 ENST00000453601.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

Genes affected

VLDLR-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VLDLR-AS1	NR_015375.2	n.429-1362G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VLDLR-AS1	ENST00000453601.5	n.429-1362G>A		intron_variant		1
VLDLR-AS1	ENST00000416826.6	n.340-1362G>A		intron_variant		2
VLDLR-AS1	ENST00000424605.5	n.288-1362G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126112 AN: 152072 Hom.: 52417 Cov.: 32

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.796

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.829 AC: 126218 AN: 152190 Hom.: 52465 Cov.: 32 AF XY: 0.836 AC XY: 62230 AN XY: 74398

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.754

Gnomad4 EAS AF: 0.981

Gnomad4 SAS AF: 0.906

Gnomad4 FIN AF: 0.876

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.817

Alfa AF: 0.809 Hom.: 6918

Bravo AF: 0.826

Asia WGS AF: 0.941 AC: 3271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.69
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs588933; hg19: chr9-2537815;