Genetic Variant VIM-AS1:n.44-616T>C (chr10-17218291-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000437232.5(VIM-AS1):n.44-616T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,006 control chromosomes in the GnomAD database, including 13,922 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 0.42 ( 13922 hom., cov: 32)

Consequence

VIM-AS1
ENST00000437232.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.557

Publications

45 publications found

Variant links:

Genes affected

VIM-AS1 (HGNC:44879): (VIM antisense RNA 1)

VIM-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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VIM-AS1	NR_108060.1 link	n.44-616T>C		intron_variant	Intron 1 of 3
VIM-AS1	NR_108061.1 link	n.642-2017T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
VIM-AS1	ENST00000437232.5 link	n.44-616T>C	intron_variant	Intron 1 of 3	2
VIM-AS1	ENST00000605833.3 link	n.686-2017T>C	intron_variant	Intron 1 of 2	3
VIM-AS1	ENST00000661048.2 link	n.479-2927T>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.421

AC:

63988

AN:

151888

Hom.:

13921

Cov.:

show subpopulations

Gnomad AFR

AF:

0.361

Gnomad AMI

AF:

0.229

Gnomad AMR

AF:

0.390

Gnomad ASJ

AF:

0.625

Gnomad EAS

AF:

0.681

Gnomad SAS

AF:

0.608

Gnomad FIN

AF:

0.407

Gnomad MID

AF:

0.554

Gnomad NFE

AF:

0.425

Gnomad OTH

AF:

0.453

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

GnomAD4 genome

AF:

0.421

AC:

64019

AN:

152006

Hom.:

13922

Cov.:

AF XY:

0.426

AC XY:

31659

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.361

AC:

14974

AN:

41462

American (AMR)

AF:

0.390

AC:

5963

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.625

AC:

2167

AN:

3468

East Asian (EAS)

AF:

0.682

AC:

3508

AN:

5146

South Asian (SAS)

AF:

0.608

AC:

2929

AN:

4816

European-Finnish (FIN)

AF:

0.407

AC:

4297

AN:

10568

Middle Eastern (MID)

AF:

0.548

AC:

161

AN:

294

European-Non Finnish (NFE)

AF:

0.425

AC:

28854

AN:

67950

Other (OTH)

AF:

0.454

AC:

958

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1880

3760

5640

7520

9400

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

624

1248

1872

2496

3120

<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:

0.434

Hom.:

47187

Bravo

AF:

0.413

Asia WGS

AF:

0.592

AC:

2059

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.51

(source)

DANN

Benign

0.29

PhyloP100

-0.56

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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