9-2548556-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453601.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VLDLR-AS1	NR_015375.2		n.275-9004G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VLDLR-AS1	ENST00000453601.5	TSL:1	n.275-9004G>A		intron	N/A
	VLDLR-AS1	ENST00000416826.6	TSL:2	n.186-9004G>A		intron	N/A
	VLDLR-AS1	ENST00000424605.5	TSL:2	n.134-9004G>A		intron	N/A

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

African (AFR) AF: 0.202 AC: 8370 AN: 41460

American (AMR) AF: 0.252 AC: 3856 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0825 AC: 286 AN: 3468

East Asian (EAS) AF: 0.427 AC: 2211 AN: 5172

South Asian (SAS) AF: 0.130 AC: 623 AN: 4806

European-Finnish (FIN) AF: 0.126 AC: 1328 AN: 10562

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9139 AN: 67972

Other (OTH) AF: 0.164 AC: 346 AN: 2110

Alfa AF: 0.150 Hom.: 5855

Bravo AF: 0.187

Asia WGS AF: 0.327 AC: 1134 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.88
DANN	Benign	0.70
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs10812227; hg19: chr9-2548556;