dbSNP rs2168136: VLDLR-AS1:n.274+27523G>A (chr9-2594577-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000453601.5(VLDLR-AS1):n.274+27523G>A variant causes a intron 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
ENST00000453601.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.357

Publications

3 publications found

Variant links:

Genes affected

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

VLDLR-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
VLDLR-AS1	NR_015375.2 link	n.274+27523G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
VLDLR-AS1	ENST00000453601.5 link	n.274+27523G>A	intron_variant	Intron 1 of 3	1
VLDLR-AS1	ENST00000416826.6 link	n.185+26652G>A	intron_variant	Intron 1 of 10	2
VLDLR-AS1	ENST00000447278.2 link	n.158+26652G>A	intron_variant	Intron 1 of 9	3

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15417

AN:

152036

Hom.:

809

Cov.:

show subpopulations

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.:

AF XY:

0.102

AC XY:

7554

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.0765

AC:

3178

AN:

41520

American (AMR)

AF:

0.123

AC:

1880

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.118

AC:

408

AN:

3468

East Asian (EAS)

AF:

0.0166

AC:

AN:

5188

South Asian (SAS)

AF:

0.0755

AC:

365

AN:

4832

European-Finnish (FIN)

AF:

0.144

AC:

1524

AN:

10568

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.113

AC:

7671

AN:

67982

Other (OTH)

AF:

0.0975

AC:

206

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

707

1414

2120

2827

3534

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

166

332

498

664

830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.111

Hom.:

542

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

(source)

DANN

Benign

0.40

PhyloP100

-0.36

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over