Genetic Variant VLDLR-AS1:n.985+183C>A (chr9-2506236-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000416826.6(VLDLR-AS1):n.985+183C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,048 control chromosomes in the GnomAD database, including 2,863 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 0.19 ( 2863 hom., cov: 32)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

VLDLR-AS1
ENST00000416826.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.129

Publications

3 publications found

Variant links:

Genes affected

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

VLDLR-AS1 links:

LOC101930053 (HGNC:):

LOC101930053 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101930053	XR_007061396.1 link	n.118+183C>A		intron_variant	Intron 1 of 3
LOC101930053	XR_007061397.1 link	n.118+183C>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
VLDLR-AS1	ENST00000416826.6 link	n.985+183C>A	intron_variant	Intron 7 of 10	2
VLDLR-AS1	ENST00000447278.2 link	n.683+183C>A	intron_variant	Intron 5 of 9	3
VLDLR-AS1	ENST00000648733.1 link	n.958+183C>A	intron_variant	Intron 7 of 11

Frequencies

GnomAD3 genomes

AF:

0.186

AC:

28276

AN:

151928

Hom.:

2862

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.192

Gnomad AMR

AF:

0.188

Gnomad ASJ

AF:

0.198

Gnomad EAS

AF:

0.382

Gnomad SAS

AF:

0.189

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.239

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.197

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.825

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.186

AC:

28274

AN:

152046

Hom.:

2863

Cov.:

AF XY:

0.185

AC XY:

13782

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.135

AC:

5605

AN:

41458

American (AMR)

AF:

0.187

AC:

2858

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.198

AC:

686

AN:

3466

East Asian (EAS)

AF:

0.382

AC:

1976

AN:

5176

South Asian (SAS)

AF:

0.189

AC:

912

AN:

4820

European-Finnish (FIN)

AF:

0.174

AC:

1837

AN:

10558

Middle Eastern (MID)

AF:

0.243

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.202

AC:

13730

AN:

67974

Other (OTH)

AF:

0.201

AC:

424

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1177

2354

3530

4707

5884

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

310

620

930

1240

1550

<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:

0.178

Hom.:

1460

Bravo

AF:

0.186

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.3

(source)

DANN

Benign

0.45

PhyloP100

-0.13

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