Variant 17-66877389-T-C details in Genebe, Genetics Data Aggregator

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

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]

CACNG5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

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

Synonymous conserved (PhyloP=-1.6 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNG5	NM_145811.3 linkuse as main transcript	c.57T>C	p.Cys19=	synonymous_variant	2/6	ENST00000533854.6	NP_665810.1
CACNG5	NM_001371476.1 linkuse as main transcript	c.57T>C	p.Cys19=	synonymous_variant	2/5		NP_001358405.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
CACNG5	ENST00000533854.6 linkuse as main transcript	c.57T>C	p.Cys19=	synonymous_variant	2/6	2	NM_145811.3	ENSP00000436836	P1
CACNG5	ENST00000307139.4 linkuse as main transcript	c.57T>C	p.Cys19=	synonymous_variant	1/5	1		ENSP00000303092	P1
CACNG5	ENST00000673855.1 linkuse as main transcript	c.57T>C	p.Cys19=	synonymous_variant	1/4			ENSP00000501267

Frequencies

GnomAD3 genomes

AF:

0.00533

AC:

811

AN:

152148

Hom.:

Cov.:

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.:

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.:

Cov.:

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

AF:

0.00533

AC:

811

AN:

152266

Hom.:

Cov.:

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.:

Bravo

AF:

0.00476

Asia WGS

AF:

0.000577

AC:

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 submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Mar 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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over