chr9-2534779-A-G

Position:

• chr9-2534779-A-G

Variant summary

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

The ENST00000657742.1(VLDLR-AS1):​n.523+1580T>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 0.105 in 152,296 control chromosomes in the GnomAD database, including 918 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 (918 hom., cov: 33)
• Consequence: VLDLR-AS1 ENST00000657742.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

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=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VLDLR-AS1	ENST00000657742.1	n.523+1580T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15972 AN: 152178 Hom.: 916 Cov.: 33

Gnomad AFR AF: 0.0916

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0822

Gnomad EAS AF: 0.0165

Gnomad SAS AF: 0.0641

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0924

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

GnomAD4 genome AF: 0.105 AC: 15991 AN: 152296 Hom.: 918 Cov.: 33 AF XY: 0.105 AC XY: 7808 AN XY: 74460

Gnomad4 AFR AF: 0.0916

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0822

Gnomad4 EAS AF: 0.0166

Gnomad4 SAS AF: 0.0639

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0915

Alfa AF: 0.112 Hom.: 1270

Bravo AF: 0.105

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.6
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1996055; hg19: chr9-2534779; COSMIC: COSV69613587;