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GeneBe

17-66877389-T-C

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_145811.3(CACNG5):c.57T>C(p.Cys19=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00577 in 1,614,138 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0053 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0058 ( 27 hom. )

Consequence

CACNG5
NM_145811.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.60
Variant links:
Genes affected
CACNG5 (HGNC:1409): (calcium voltage-gated channel auxiliary subunit gamma 5) The protein encoded by this gene is a type II transmembrane AMPA receptor regulatory protein (TARP). TARPs regulate both trafficking and channel gating of the AMPA receptors. This gene is part of a functionally diverse eight-member protein subfamily of the PMP-22/EMP/MP20 family and is located in a cluster with two family members, a type I TARP and a calcium channel gamma subunit. This gene is a susceptibility locus for schizophrenia and bipolar disorder. [provided by RefSeq, Dec 2010]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-66877389-T-C is Benign according to our data. Variant chr17-66877389-T-C is described in ClinVar as [Benign]. Clinvar id is 719521.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.6 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CACNG5NM_145811.3 linkuse as main transcriptc.57T>C p.Cys19= synonymous_variant 2/6 ENST00000533854.6
CACNG5NM_001371476.1 linkuse as main transcriptc.57T>C p.Cys19= synonymous_variant 2/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CACNG5ENST00000533854.6 linkuse as main transcriptc.57T>C p.Cys19= synonymous_variant 2/62 NM_145811.3 P1
CACNG5ENST00000307139.4 linkuse as main transcriptc.57T>C p.Cys19= synonymous_variant 1/51 P1
CACNG5ENST00000673855.1 linkuse as main transcriptc.57T>C p.Cys19= synonymous_variant 1/4

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00533
AC:
811
AN:
152148
Hom.:
4
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00142
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0101
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0129
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00651
Gnomad OTH
AF:
0.00766
GnomAD3 exomes
AF:
0.00522
AC:
1311
AN:
251332
Hom.:
3
AF XY:
0.00501
AC XY:
681
AN XY:
135842
show subpopulations
Gnomad AFR exome
AF:
0.00123
Gnomad AMR exome
AF:
0.00442
Gnomad ASJ exome
AF:
0.000794
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000196
Gnomad FIN exome
AF:
0.0122
Gnomad NFE exome
AF:
0.00726
Gnomad OTH exome
AF:
0.00571
GnomAD4 exome
AF:
0.00582
AC:
8505
AN:
1461872
Hom.:
27
Cov.:
31
AF XY:
0.00552
AC XY:
4012
AN XY:
727240
show subpopulations
Gnomad4 AFR exome
AF:
0.000866
Gnomad4 AMR exome
AF:
0.00470
Gnomad4 ASJ exome
AF:
0.000804
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.000139
Gnomad4 FIN exome
AF:
0.0119
Gnomad4 NFE exome
AF:
0.00656
Gnomad4 OTH exome
AF:
0.00492
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00533
AC:
811
AN:
152266
Hom.:
4
Cov.:
32
AF XY:
0.00564
AC XY:
420
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.00142
Gnomad4 AMR
AF:
0.0101
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0129
Gnomad4 NFE
AF:
0.00651
Gnomad4 OTH
AF:
0.00758
Alfa
AF:
0.00515
Hom.:
2
Bravo
AF:
0.00476
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.00616
EpiControl
AF:
0.00658

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeMar 29, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
Cadd
Benign
1.9
Dann
Benign
0.54

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.

Other links and lift over

dbSNP: rs146874664; hg19: chr17-64873507; API