9-2548556-C-T

Variant names:

• chr9-2548556-C-T
• rs10812227
• ENST00000453601.5:n.275-9004G>A

Variant summary

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

The ENST00000453601.5(VLDLR-AS1):​n.275-9004G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,044 control chromosomes in the GnomAD database, including 2,652 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 0.17 (2652 hom., cov: 33)
• Consequence: VLDLR-AS1 ENST00000453601.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VLDLR-AS1	NR_015375.2	n.275-9004G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VLDLR-AS1	ENST00000453601.5	n.275-9004G>A		intron_variant	Intron 1 of 3	1
VLDLR-AS1	ENST00000416826.6	n.186-9004G>A		intron_variant	Intron 1 of 10	2
VLDLR-AS1	ENST00000424605.5	n.134-9004G>A		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26218 AN: 151926 Hom.: 2640 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.0825

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.173 AC: 26277 AN: 152044 Hom.: 2652 Cov.: 33 AF XY: 0.177 AC XY: 13168 AN XY: 74312

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.0825

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.164

Alfa AF: 0.132 Hom.: 1404

Bravo AF: 0.187

Asia WGS AF: 0.327 AC: 1134 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.88
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10812227; hg19: chr9-2548556;