9-2382952-G-T

Variant names:

• chr9-2382952-G-T
• rs1331829
• ENST00000742983.1:n.898+2658C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000742983.1(VLDLR-AS1):​n.898+2658C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 151,848 control chromosomes in the GnomAD database, including 20,381 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 0.51 (20381 hom., cov: 32)
• Consequence: VLDLR-AS1 ENST00000742983.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000742983.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VLDLR-AS1	ENST00000742983.1		n.898+2658C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77622 AN: 151730 Hom.: 20361 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.512 AC: 77682 AN: 151848 Hom.: 20381 Cov.: 32 AF XY: 0.510 AC XY: 37875 AN XY: 74220

African (AFR) AF: 0.636 AC: 26348 AN: 41418

American (AMR) AF: 0.499 AC: 7610 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1690 AN: 3468

East Asian (EAS) AF: 0.608 AC: 3128 AN: 5142

South Asian (SAS) AF: 0.506 AC: 2437 AN: 4816

European-Finnish (FIN) AF: 0.436 AC: 4587 AN: 10524

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30249 AN: 67906

Other (OTH) AF: 0.523 AC: 1103 AN: 2110

Alfa AF: 0.489 Hom.: 4115

Bravo AF: 0.520

Asia WGS AF: 0.566 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
DANN	Benign	0.34
PhyloP100		-0.71

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: rs1331829;

hg19: chr9-2382952;

COSMIC: COSV69443179;