2-17620917-G-A

Position:

• chr2-17620917-G-A

Variant summary

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

The NM_003385.5(VSNL1):​c.163-28493G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,108 control chromosomes in the GnomAD database, including 4,535 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 0.24 (4535 hom., cov: 32)
• Consequence: VSNL1 NM_003385.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VSNL1	NM_003385.5	c.163-28493G>A		intron_variant		ENST00000295156.9	NP_003376.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VSNL1	ENST00000295156.9	c.163-28493G>A		intron_variant		1	NM_003385.5	ENSP00000295156.4
VSNL1	ENST00000404666.6	c.163-28493G>A		intron_variant		3		ENSP00000384014.1

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35882 AN: 151990 Hom.: 4536 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.0117

Gnomad SAS AF: 0.0773

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.236 AC: 35897 AN: 152108 Hom.: 4535 Cov.: 32 AF XY: 0.229 AC XY: 17054 AN XY: 74330

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.0116

Gnomad4 SAS AF: 0.0778

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.245

Alfa AF: 0.264 Hom.: 2798

Bravo AF: 0.232

Asia WGS AF: 0.0570 AC: 200 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.5
DANN	Benign	0.51

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: rs11677051; hg19: chr2-17802184;