Variant rs2070611 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001282907.2(CCT8):c.-228C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 1,607,270 control chromosomes in the GnomAD database, including 13,724 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 0.16 ( 2209 hom., cov: 33)

Exomes 𝑓: 0.12 ( 11515 hom. )

Consequence

CCT8
NM_001282907.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.607

Variant links:

Genes affected

CCT8 (HGNC:1623): (chaperonin containing TCP1 subunit 8) This gene encodes the theta subunit of the CCT chaperonin, which is abundant in the eukaryotic cytosol and may be involved in the transport and assembly of newly synthesized proteins. Alternative splicing results in multiple transcript variants of this gene. A pseudogene related to this gene is located on chromosome 1. [provided by RefSeq, Sep 2013]

CCT8 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCT8	NM_006585.4 link	c.60+78C>G		intron_variant		ENST00000286788.9	NP_006576.2	P50990-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCT8	ENST00000286788.9 link	c.60+78C>G		intron_variant		1	NM_006585.4	ENSP00000286788.4		P50990-1

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23953

AN:

152102

Hom.:

2208

Cov.:

show subpopulations

Gnomad AFR

AF:

0.258

Gnomad AMI

AF:

0.0429

Gnomad AMR

AF:

0.165

Gnomad ASJ

AF:

0.131

Gnomad EAS

AF:

0.147

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.0652

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.157

GnomAD4 exome

AF:

0.121

AC:

176551

AN:

1455048

Hom.:

11515

Cov.:

AF XY:

0.120

AC XY:

86735

AN XY:

723352

show subpopulations

Gnomad4 AFR exome

AF:

0.270

Gnomad4 AMR exome

AF:

0.176

Gnomad4 ASJ exome

AF:

0.131

Gnomad4 EAS exome

AF:

0.103

Gnomad4 SAS exome

AF:

0.112

Gnomad4 FIN exome

AF:

0.0704

Gnomad4 NFE exome

AF:

0.117

Gnomad4 OTH exome

AF:

0.139

GnomAD4 genome

AF:

0.157

AC:

23973

AN:

152222

Hom.:

2209

Cov.:

AF XY:

0.153

AC XY:

11418

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.258

Gnomad4 AMR

AF:

0.165

Gnomad4 ASJ

AF:

0.131

Gnomad4 EAS

AF:

0.146

Gnomad4 SAS

AF:

0.121

Gnomad4 FIN

AF:

0.0652

Gnomad4 NFE

AF:

0.115

Gnomad4 OTH

AF:

0.158

Alfa

AF:

0.144

Hom.:

231

Bravo

AF:

0.169

Asia WGS

AF:

0.149

AC:

520

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

5.6

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over