Genetic Variant VSNL1:c.-6+469G>A (chr2-17541387-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_003385.5(VSNL1):c.-6+469G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,122 control chromosomes in the GnomAD database, including 8,307 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 0.29 ( 8307 hom., cov: 32)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

VSNL1
NM_003385.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.15

Publications

4 publications found

Variant links:

Genes affected

VSNL1 (HGNC:12722): (visinin like 1) This gene is a member of the visinin/recoverin subfamily of neuronal calcium sensor proteins. The encoded protein is strongly expressed in granule cells of the cerebellum where it associates with membranes in a calcium-dependent manner and modulates intracellular signaling pathways of the central nervous system by directly or indirectly regulating the activity of adenylyl cyclase. Alternatively spliced transcript variants have been observed, but their full-length nature has not been determined. [provided by RefSeq, Jul 2008]

VSNL1 links:

ENSG00000308172 (HGNC:):

ENSG00000308172 links:

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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=-0.62).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003385.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
VSNL1	NM_003385.5	MANE Select	c.-6+469G>A	intron	N/A	NP_003376.2
VSNL1	NM_001366804.2		c.-6+469G>A	intron	N/A	NP_001353733.1
VSNL1	NM_001366803.2		c.-6+1205G>A	intron	N/A	NP_001353732.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
VSNL1	ENST00000295156.9	TSL:1 MANE Select	c.-6+469G>A	intron	N/A	ENSP00000295156.4
VSNL1	ENST00000404666.6	TSL:3	c.-6+1985G>A	intron	N/A	ENSP00000384014.1
VSNL1	ENST00000406397.1	TSL:5	c.-298G>A	5_prime_UTR	Exon 1 of 4	ENSP00000384719.1

Frequencies

GnomAD3 genomes

AF:

0.292

AC:

44399

AN:

152002

Hom.:

8293

Cov.:

show subpopulations

Gnomad AFR

AF:

0.149

Gnomad AMI

AF:

0.186

Gnomad AMR

AF:

0.442

Gnomad ASJ

AF:

0.234

Gnomad EAS

AF:

0.869

Gnomad SAS

AF:

0.418

Gnomad FIN

AF:

0.410

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.290

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

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)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.292

AC:

44437

AN:

152120

Hom.:

8307

Cov.:

AF XY:

0.306

AC XY:

22732

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.149

AC:

6198

AN:

41516

American (AMR)

AF:

0.443

AC:

6767

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.234

AC:

811

AN:

3470

East Asian (EAS)

AF:

0.869

AC:

4489

AN:

5168

South Asian (SAS)

AF:

0.417

AC:

2008

AN:

4818

European-Finnish (FIN)

AF:

0.410

AC:

4338

AN:

10580

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.280

AC:

18999

AN:

67964

Other (OTH)

AF:

0.296

AC:

623

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1446

2892

4337

5783

7229

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

454

908

1362

1816

2270

<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:

0.294

Hom.:

5867

Bravo

AF:

0.291

Asia WGS

AF:

0.615

AC:

2136

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

(source)

DANN

Benign

0.90

PhyloP100

1.2

PromoterAI

-0.0074

Neutral

(source)

Mutation Taster

=299/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over