chr5-10263470-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_012073.5(CCT5):​c.1498+156G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,188 control chromosomes in the GnomAD database, including 3,816 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 3816 hom., cov: 34)

Consequence

CCT5
NM_012073.5 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.700
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 5-10263470-G-A is Benign according to our data. Variant chr5-10263470-G-A is described in ClinVar as [Benign]. Clinvar id is 1228359.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CCT5NM_012073.5 linkuse as main transcriptc.1498+156G>A intron_variant ENST00000280326.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CCT5ENST00000280326.9 linkuse as main transcriptc.1498+156G>A intron_variant 1 NM_012073.5 P1P48643-1

Frequencies

GnomAD3 genomes
AF:
0.155
AC:
23613
AN:
152070
Hom.:
3817
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.415
Gnomad AMI
AF:
0.0351
Gnomad AMR
AF:
0.0757
Gnomad ASJ
AF:
0.0592
Gnomad EAS
AF:
0.0304
Gnomad SAS
AF:
0.0666
Gnomad FIN
AF:
0.0766
Gnomad MID
AF:
0.0981
Gnomad NFE
AF:
0.0507
Gnomad OTH
AF:
0.126
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.155
AC:
23638
AN:
152188
Hom.:
3816
Cov.:
34
AF XY:
0.152
AC XY:
11280
AN XY:
74418
show subpopulations
Gnomad4 AFR
AF:
0.415
Gnomad4 AMR
AF:
0.0755
Gnomad4 ASJ
AF:
0.0592
Gnomad4 EAS
AF:
0.0305
Gnomad4 SAS
AF:
0.0654
Gnomad4 FIN
AF:
0.0766
Gnomad4 NFE
AF:
0.0507
Gnomad4 OTH
AF:
0.125
Alfa
AF:
0.0652
Hom.:
921
Bravo
AF:
0.167
Asia WGS
AF:
0.0810
AC:
283
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxJun 18, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.14
DANN
Benign
0.32

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: rs2292267; hg19: chr5-10263582; API