Variant rs1054879 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014286.4(NCS1):c.*517G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 152,356 control chromosomes in the GnomAD database, including 16,379 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 0.45 ( 16304 hom., cov: 31)

Exomes 𝑓: 0.59 ( 75 hom. )

Consequence

NCS1
NM_014286.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.33

Variant links:

Genes affected

NCS1 (HGNC:3953): (neuronal calcium sensor 1) This gene is a member of the neuronal calcium sensor gene family, which encode calcium-binding proteins expressed predominantly in neurons. The protein encoded by this gene regulates G protein-coupled receptor phosphorylation in a calcium-dependent manner and can substitute for calmodulin. The protein is associated with secretory granules and modulates synaptic transmission and synaptic plasticity. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

NCS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NCS1	NM_014286.4 link	c.*517G>A		3_prime_UTR_variant	8/8	ENST00000372398.6	NP_055101.2	P62166-1A0A024R8B2
NCS1	NM_001128826.2 link	c.*517G>A		3_prime_UTR_variant	8/8		NP_001122298.1	P62166-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NCS1	ENST00000372398.6 link	c.*517G>A		3_prime_UTR_variant	8/8	1	NM_014286.4	ENSP00000361475.3		P62166-1

Frequencies

GnomAD3 genomes

AF:

0.449

AC:

68202

AN:

151814

Hom.:

16303

Cov.:

show subpopulations

Gnomad AFR

AF:

0.310

Gnomad AMI

AF:

0.501

Gnomad AMR

AF:

0.435

Gnomad ASJ

AF:

0.658

Gnomad EAS

AF:

0.198

Gnomad SAS

AF:

0.604

Gnomad FIN

AF:

0.585

Gnomad MID

AF:

0.576

Gnomad NFE

AF:

0.511

Gnomad OTH

AF:

0.486

GnomAD4 exome

AF:

0.595

AC:

251

AN:

422

Hom.:

Cov.:

AF XY:

0.577

AC XY:

143

AN XY:

248

show subpopulations

Gnomad4 FIN exome

AF:

0.594

Gnomad4 NFE exome

AF:

0.500

Gnomad4 OTH exome

AF:

0.667

GnomAD4 genome

AF:

0.449

AC:

68234

AN:

151934

Hom.:

16304

Cov.:

AF XY:

0.454

AC XY:

33717

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.310

Gnomad4 AMR

AF:

0.435

Gnomad4 ASJ

AF:

0.658

Gnomad4 EAS

AF:

0.197

Gnomad4 SAS

AF:

0.604

Gnomad4 FIN

AF:

0.585

Gnomad4 NFE

AF:

0.511

Gnomad4 OTH

AF:

0.487

Alfa

AF:

0.465

Hom.:

4809

Bravo

AF:

0.426

Asia WGS

AF:

0.417

AC:

1448

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

2.0

DANN

Benign

0.72

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over