5-10264850-A-G

Variant names:

• chr5-10264850-A-G
• rs544
• NM_012073.5:c.*67A>G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_012073.5(CCT5):​c.*67A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 1,591,202 control chromosomes in the GnomAD database, including 549,137 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.74 (43755 hom., cov: 32)
  • Exomes 𝑓: 0.83 (505382 hom.)
• Consequence: CCT5 NM_012073.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -0.0910

Genes affected

CCT5 (HGNC:1618): (chaperonin containing TCP1 subunit 5) 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. Mutations in this gene cause hereditary sensory and autonomic neuropathy with spastic paraplegia (HSNSP). Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 5 and 13. [provided by RefSeq, Apr 2015]

ENSG00000271980 (HGNC:58210):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 5-10264850-A-G is Benign according to our data. Variant chr5-10264850-A-G is described in ClinVar as [Benign]. Clinvar id is 350262.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-10264850-A-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCT5	NM_012073.5	c.*67A>G		3_prime_UTR_variant	Exon 11 of 11	ENST00000280326.9	NP_036205.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCT5	ENST00000280326.9	c.*67A>G		3_prime_UTR_variant	Exon 11 of 11	1	NM_012073.5	ENSP00000280326.4

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112372 AN: 152050 Hom.: 43738 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.767

GnomAD4 exome AF: 0.834 AC: 1200497 AN: 1439034 Hom.: 505382 Cov.: 25 AF XY: 0.830 AC XY: 595408 AN XY: 717164

Gnomad4 AFR exome AF: 0.448

Gnomad4 AMR exome AF: 0.801

Gnomad4 ASJ exome AF: 0.872

Gnomad4 EAS exome AF: 0.890

Gnomad4 SAS exome AF: 0.664

Gnomad4 FIN exome AF: 0.862

Gnomad4 NFE exome AF: 0.857

Gnomad4 OTH exome AF: 0.823

GnomAD4 genome AF: 0.739 AC: 112429 AN: 152168 Hom.: 43755 Cov.: 32 AF XY: 0.742 AC XY: 55212 AN XY: 74396

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.859

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.768

Alfa AF: 0.799 Hom.: 11093

Bravo AF: 0.728

Asia WGS AF: 0.773 AC: 2684 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary sensory and autonomic neuropathy with spastic paraplegia Benign:2

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:2

Jun 18, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.055
DANN	Benign	0.66
RBP_binding_hub_radar		0.97
RBP_regulation_power_radar		2.1

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

Other links and lift over

dbSNP: rs544; hg19: chr5-10264962;