rs10113968

chr9-2455202-T-G

Variant summary

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

The ENST00000657742.1(VLDLR-AS1):n.1258-30692A>C 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 0.472 in 151,856 control chromosomes in the GnomAD database, including 17,529 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 0.47 (17529 hom., cov: 32)
• Consequence: VLDLR-AS1 ENST00000657742.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

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

LOC101930053 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101930053	XR_001746603.2	n.394-2211A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VLDLR-AS1	ENST00000657742.1	n.1258-30692A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71663 AN: 151736 Hom.: 17507 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.472 AC: 71733 AN: 151856 Hom.: 17529 Cov.: 32 AF XY: 0.470 AC XY: 34859 AN XY: 74218

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.460

Alfa AF: 0.502 Hom.: 8234

Bravo AF: 0.459

Asia WGS AF: 0.290 AC: 1009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	8.2
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10113968; hg19: chr9-2455202;