chr9-130226430-T-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_014286.4(NCS1):c.516T>G(p.Gly172=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 1,612,954 control chromosomes in the GnomAD database, including 89,139 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 0.36 ( 10122 hom., cov: 32)
Exomes 𝑓: 0.32 ( 79017 hom. )
Consequence
NCS1
NM_014286.4 synonymous
NM_014286.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.37
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP7
?
Synonymous conserved (PhyloP=-1.37 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCS1 | NM_014286.4 | c.516T>G | p.Gly172= | synonymous_variant | 7/8 | ENST00000372398.6 | |
NCS1 | NM_001128826.2 | c.462T>G | p.Gly154= | synonymous_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCS1 | ENST00000372398.6 | c.516T>G | p.Gly172= | synonymous_variant | 7/8 | 1 | NM_014286.4 | P1 | |
NCS1 | ENST00000630865.1 | c.462T>G | p.Gly154= | synonymous_variant | 7/8 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.356 AC: 53977AN: 151732Hom.: 10095 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
53977
AN:
151732
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.329 AC: 82493AN: 250692Hom.: 15060 AF XY: 0.314 AC XY: 42557AN XY: 135498
GnomAD3 exomes
AF:
AC:
82493
AN:
250692
Hom.:
AF XY:
AC XY:
42557
AN XY:
135498
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.323 AC: 471662AN: 1461104Hom.: 79017 Cov.: 37 AF XY: 0.318 AC XY: 231377AN XY: 726846
GnomAD4 exome
AF:
AC:
471662
AN:
1461104
Hom.:
Cov.:
37
AF XY:
AC XY:
231377
AN XY:
726846
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.356 AC: 54048AN: 151850Hom.: 10122 Cov.: 32 AF XY: 0.347 AC XY: 25762AN XY: 74186
GnomAD4 genome
?
AF:
AC:
54048
AN:
151850
Hom.:
Cov.:
32
AF XY:
AC XY:
25762
AN XY:
74186
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
798
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at