rs12237653

chr9-2551654-T-C

Variant summary

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

The NR_015375.2(VLDLR-AS1):n.275-12102A>G 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 0.173 in 152,132 control chromosomes in the GnomAD database, including 2,641 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 (2641 hom., cov: 32)
• Consequence: VLDLR-AS1 NR_015375.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VLDLR-AS1	NR_015375.2	n.275-12102A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VLDLR-AS1	ENST00000657742.1	n.275-12102A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26190 AN: 152014 Hom.: 2630 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.0868

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.173 AC: 26243 AN: 152132 Hom.: 2641 Cov.: 32 AF XY: 0.178 AC XY: 13246 AN XY: 74370

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.0868

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.169

Alfa AF: 0.148 Hom.: 1729

Bravo AF: 0.185

Asia WGS AF: 0.354 AC: 1228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.4
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12237653; hg19: chr9-2551654;