Variant 8-67149947-CTTTTTTTTTTTTTTT-CTTTTTTTTTTTTTT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001382391.1(CSPP1):c.2128+36delT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.85 ( 32231 hom., cov: 0)

Exomes 𝑓: 0.36 ( 902 hom. )

Failed GnomAD Quality Control

Consequence

CSPP1
NM_001382391.1 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.26

Variant links:

Genes affected

CSPP1 (HGNC:26193): (centrosome and spindle pole associated protein 1) This gene encodes a centrosome and spindle pole associated protein. The encoded protein plays a role in cell-cycle progression and spindle organization, regulates cytokinesis, interacts with Nephrocystin 8 and is required for cilia formation. Mutations in this gene result in primary cilia abnormalities and classical Joubert syndrome. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Apr 2014]

CSPP1 links:

CSPP1 (HGNC:):

CSPP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 8-67149947-CT-C is Benign according to our data. Variant chr8-67149947-CT-C is described in ClinVar as [Benign]. Clinvar id is 402568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149947-CT-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSPP1	NM_001382391.1 linkuse as main transcript	c.2128+36delT		intron_variant		ENST00000678616.1	NP_001369320.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSPP1	ENST00000678616.1 linkuse as main transcript	c.2128+36delT		intron_variant			NM_001382391.1	ENSP00000504733.1		A0A7I2V5W3

Frequencies

GnomAD3 genomes

AF:

0.852

AC:

76325

AN:

89560

Hom.:

32244

Cov.:

show subpopulations

Gnomad AFR

AF:

0.865

Gnomad AMI

AF:

0.902

Gnomad AMR

AF:

0.841

Gnomad ASJ

AF:

0.870

Gnomad EAS

AF:

0.768

Gnomad SAS

AF:

0.857

Gnomad FIN

AF:

0.707

Gnomad MID

AF:

0.844

Gnomad NFE

AF:

0.861

Gnomad OTH

AF:

0.856

GnomAD3 exomes

AF:

0.0590

AC:

3945

AN:

66916

Hom.:

AF XY:

0.0560

AC XY:

2032

AN XY:

36278

show subpopulations

Gnomad AFR exome

AF:

0.0603

Gnomad AMR exome

AF:

0.102

Gnomad ASJ exome

AF:

0.0898

Gnomad EAS exome

AF:

0.0770

Gnomad SAS exome

AF:

0.0698

Gnomad FIN exome

AF:

0.0598

Gnomad NFE exome

AF:

0.0461

Gnomad OTH exome

AF:

0.0842

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.361

AC:

372791

AN:

1032604

Hom.:

902

Cov.:

AF XY:

0.355

AC XY:

180785

AN XY:

509386

show subpopulations

Gnomad4 AFR exome

AF:

0.352

Gnomad4 AMR exome

AF:

0.203

Gnomad4 ASJ exome

AF:

0.333

Gnomad4 EAS exome

AF:

0.301

Gnomad4 SAS exome

AF:

0.270

Gnomad4 FIN exome

AF:

0.210

Gnomad4 NFE exome

AF:

0.379

Gnomad4 OTH exome

AF:

0.358

GnomAD4 genome

AF:

0.852

AC:

76296

AN:

89530

Hom.:

32231

Cov.:

AF XY:

0.844

AC XY:

34758

AN XY:

41204

show subpopulations

Gnomad4 AFR

AF:

0.865

Gnomad4 AMR

AF:

0.841

Gnomad4 ASJ

AF:

0.870

Gnomad4 EAS

AF:

0.768

Gnomad4 SAS

AF:

0.856

Gnomad4 FIN

AF:

0.707

Gnomad4 NFE

AF:

0.861

Gnomad4 OTH

AF:

0.856

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Joubert syndrome 21

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 19, 2024

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 17, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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