chr2-17544008-A-G

Position:

• chr2-17544008-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003385.5(VSNL1):​c.-6+3090A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,962 control chromosomes in the GnomAD database, including 8,310 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 (8310 hom., cov: 32)
• Consequence: VSNL1 NM_003385.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VSNL1	NM_003385.5	c.-6+3090A>G		intron_variant		ENST00000295156.9	NP_003376.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VSNL1	ENST00000295156.9	c.-6+3090A>G		intron_variant		1	NM_003385.5	ENSP00000295156.4
VSNL1	ENST00000404666.6	c.-6+4606A>G		intron_variant		3		ENSP00000384014.1

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44424 AN: 151844 Hom.: 8296 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.293 AC: 44468 AN: 151962 Hom.: 8310 Cov.: 32 AF XY: 0.306 AC XY: 22734 AN XY: 74252

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.295

Alfa AF: 0.288 Hom.: 3184

Bravo AF: 0.292

Asia WGS AF: 0.617 AC: 2145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.73

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

LitVar

Other links and lift over

dbSNP: rs834504; hg19: chr2-17725275;