rs4038131

Positions:

• chr2-17593765-A-G
• chr2-17593765-A-T

Variant summary

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

The NM_003385.5(VSNL1):​c.162+1529A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,146 control chromosomes in the GnomAD database, including 1,288 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 0.12 (1288 hom., cov: 32)
• Consequence: VSNL1 NM_003385.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VSNL1	NM_003385.5	c.162+1529A>G		intron_variant		ENST00000295156.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VSNL1	ENST00000295156.9	c.162+1529A>G		intron_variant		1	NM_003385.5	P1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17894 AN: 152028 Hom.: 1287 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.0823

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0684

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0869

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.118 AC: 17921 AN: 152146 Hom.: 1288 Cov.: 32 AF XY: 0.116 AC XY: 8651 AN XY: 74384

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.0823

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.0687

Gnomad4 FIN AF: 0.0651

Gnomad4 NFE AF: 0.0870

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0931 Hom.: 587

Bravo AF: 0.124

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.40
DANN	Benign	0.63

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: rs4038131; hg19: chr2-17775032;