rs2168136

chr9-2594577-C-T

Variant summary

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

The NR_015375.2(VLDLR-AS1):n.274+27523G>A variant causes a intron, non coding transcript 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 NR_015375.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VLDLR-AS1	NR_015375.2	n.274+27523G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VLDLR-AS1	ENST00000657742.1	n.274+27523G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0765

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.0166

Gnomad4 SAS AF: 0.0755

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0975

Alfa AF: 0.111 Hom.: 483

Bravo AF: 0.101

Asia WGS AF: 0.0480 AC: 166 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.72
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2168136; hg19: chr9-2594577;