rs2168136

Variant names:

• chr9-2594577-C-T
• rs2168136
• ENST00000453601.5:n.274+27523G>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.274+27523G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,154 control chromosomes in the GnomAD database, including 812 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 0.10 (812 hom., cov: 32)
• Consequence: VLDLR-AS1 ENST00000453601.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.118 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.274+27523G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VLDLR-AS1	ENST00000453601.5	TSL:1	n.274+27523G>A		intron	N/A
	VLDLR-AS1	ENST00000416826.6	TSL:2	n.185+26652G>A		intron	N/A
	VLDLR-AS1	ENST00000447278.2	TSL:3	n.158+26652G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15417 AN: 152036 Hom.: 809 Cov.: 32

Gnomad AFR AF: 0.0766

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0163

Gnomad SAS AF: 0.0744

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0986

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

GnomAD4 genome AF: 0.101 AC: 15442 AN: 152154 Hom.: 812 Cov.: 32 AF XY: 0.102 AC XY: 7554 AN XY: 74374

African (AFR) AF: 0.0765 AC: 3178 AN: 41520

American (AMR) AF: 0.123 AC: 1880 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 408 AN: 3468

East Asian (EAS) AF: 0.0166 AC: 86 AN: 5188

South Asian (SAS) AF: 0.0755 AC: 365 AN: 4832

European-Finnish (FIN) AF: 0.144 AC: 1524 AN: 10568

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7671 AN: 67982

Other (OTH) AF: 0.0975 AC: 206 AN: 2112

Alfa AF: 0.111 Hom.: 542

Bravo AF: 0.101

Asia WGS AF: 0.0480 AC: 166 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.72
DANN	Benign	0.40
PhyloP100		-0.36

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2168136;

hg19: chr9-2594577;