Variant 7-56061818-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001762.4(CCT6A):c.1419A>G(p.Ser473=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0657 in 1,606,192 control chromosomes in the GnomAD database, including 4,699 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.10 ( 1195 hom., cov: 31)

Exomes 𝑓: 0.062 ( 3504 hom. )

Consequence

CCT6A
NM_001762.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.51

Variant links:

Genes affected

CCT6A (HGNC:1620): (chaperonin containing TCP1 subunit 6A) The protein encoded by this gene is a molecular chaperone that is a member of the chaperonin containing TCP1 complex (CCT), also known as the TCP1 ring complex (TRiC). This complex consists of two identical stacked rings, each containing eight different proteins. Unfolded polypeptides enter the central cavity of the complex and are folded in an ATP-dependent manner. The complex folds various proteins, including actin and tubulin. Alternate transcriptional splice variants of this gene, encoding different isoforms, have been characterized. In addition, several pseudogenes of this gene have been located. [provided by RefSeq, Jun 2010]

CCT6A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP6

Variant 7-56061818-A-G is Benign according to our data. Variant chr7-56061818-A-G is described in ClinVar as [Benign]. Clinvar id is 1221249.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.51 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCT6A	NM_001762.4 linkuse as main transcript	c.1419A>G	p.Ser473=	synonymous_variant	12/14	ENST00000275603.9
CCT6A	NM_001009186.2 linkuse as main transcript	c.1284A>G	p.Ser428=	synonymous_variant	11/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCT6A	ENST00000275603.9 linkuse as main transcript	c.1419A>G	p.Ser473=	synonymous_variant	12/14	1	NM_001762.4	P1	P40227-1

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15371

AN:

151614

Hom.:

1191

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.0525

Gnomad ASJ

AF:

0.0852

Gnomad EAS

AF:

0.0101

Gnomad SAS

AF:

0.0598

Gnomad FIN

AF:

0.0798

Gnomad MID

AF:

0.0994

Gnomad NFE

AF:

0.0581

Gnomad OTH

AF:

0.0922

GnomAD3 exomes

AF:

0.0647

AC:

15883

AN:

245630

Hom.:

787

AF XY:

0.0630

AC XY:

8383

AN XY:

132984

show subpopulations

Gnomad AFR exome

AF:

0.212

Gnomad AMR exome

AF:

0.0350

Gnomad ASJ exome

AF:

0.0827

Gnomad EAS exome

AF:

0.00978

Gnomad SAS exome

AF:

0.0613

Gnomad FIN exome

AF:

0.0772

Gnomad NFE exome

AF:

0.0589

Gnomad OTH exome

AF:

0.0616

GnomAD4 exome

AF:

0.0620

AC:

90126

AN:

1454462

Hom.:

3504

Cov.:

AF XY:

0.0615

AC XY:

44524

AN XY:

723688

show subpopulations

Gnomad4 AFR exome

AF:

0.220

Gnomad4 AMR exome

AF:

0.0377

Gnomad4 ASJ exome

AF:

0.0841

Gnomad4 EAS exome

AF:

0.00528

Gnomad4 SAS exome

AF:

0.0638

Gnomad4 FIN exome

AF:

0.0756

Gnomad4 NFE exome

AF:

0.0584

Gnomad4 OTH exome

AF:

0.0682

GnomAD4 genome

AF:

0.101

AC:

15398

AN:

151730

Hom.:

1195

Cov.:

AF XY:

0.101

AC XY:

7458

AN XY:

74142

show subpopulations

Gnomad4 AFR

AF:

0.216

Gnomad4 AMR

AF:

0.0527

Gnomad4 ASJ

AF:

0.0852

Gnomad4 EAS

AF:

0.0101

Gnomad4 SAS

AF:

0.0604

Gnomad4 FIN

AF:

0.0798

Gnomad4 NFE

AF:

0.0580

Gnomad4 OTH

AF:

0.0912

Alfa

AF:

0.0833

Hom.:

336

Bravo

AF:

0.105

Asia WGS

AF:

0.0490

AC:

173

AN:

3478

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

GeneDx

Aug 08, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

8.2

DANN

Benign

0.79

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.16

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