NM_003385.5:c.163-28493G>A

Variant names:

• chr2-17620917-G-A
• rs11677051
• NM_003385.5:c.163-28493G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
VSNL1	NM_003385.5	c.163-28493G>A		intron_variant	Intron 2 of 3	ENST00000295156.9	NP_003376.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VSNL1	ENST00000295156.9	c.163-28493G>A		intron_variant	Intron 2 of 3	1	NM_003385.5	ENSP00000295156.4
VSNL1	ENST00000404666.6	c.163-28493G>A		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.202 AC: 8390 AN: 41500

American (AMR) AF: 0.214 AC: 3265 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 928 AN: 3470

East Asian (EAS) AF: 0.0116 AC: 60 AN: 5182

South Asian (SAS) AF: 0.0778 AC: 375 AN: 4822

European-Finnish (FIN) AF: 0.256 AC: 2712 AN: 10578

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19381 AN: 67952

Other (OTH) AF: 0.245 AC: 518 AN: 2112

Alfa AF: 0.265 Hom.: 3084

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
PhyloP100		0.42
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11677051; hg19: chr2-17802184;