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

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS1

The NM_001382391.1(CSPP1):c.2128+33_2128+36delTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0275 in 1,108,126 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0010 ( 0 hom., cov: 0)

Exomes 𝑓: 0.030 ( 0 hom. )

Consequence

CSPP1
NM_001382391.1 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0650

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:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP6

Variant 8-67149947-CTTTT-C is Benign according to our data. Variant chr8-67149947-CTTTT-C is described in ClinVar as [Likely_benign]. Clinvar id is 1219474.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-67149947-CTTTT-C is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00101 (90/89440) while in subpopulation SAS AF= 0.0322 (81/2518). AF 95% confidence interval is 0.0265. There are 0 homozygotes in gnomad4. There are 70 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSPP1	NM_001382391.1 link	c.2128+33_2128+36delTTTT		intron_variant		ENST00000678616.1	NP_001369320.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSPP1	ENST00000678616.1 link	c.2128+13_2128+16delTTTT		intron_variant			NM_001382391.1	ENSP00000504733.1		A0A7I2V5W3

Frequencies

GnomAD3 genomes

AF:

0.00101

AC:

AN:

89468

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000260

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0320

Gnomad FIN

AF:

0.000340

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000220

Gnomad OTH

AF:

0.000858

GnomAD3 exomes

AF:

0.0312

AC:

2091

AN:

66916

Hom.:

AF XY:

0.0327

AC XY:

1185

AN XY:

36278

show subpopulations

Gnomad AFR exome

AF:

0.0286

Gnomad AMR exome

AF:

0.0400

Gnomad ASJ exome

AF:

0.0272

Gnomad EAS exome

AF:

0.0322

Gnomad SAS exome

AF:

0.0439

Gnomad FIN exome

AF:

0.0445

Gnomad NFE exome

AF:

0.0263

Gnomad OTH exome

AF:

0.0344

GnomAD4 exome

AF:

0.0298

AC:

30335

AN:

1018686

Hom.:

AF XY:

0.0308

AC XY:

15482

AN XY:

502118

show subpopulations

Gnomad4 AFR exome

AF:

0.0343

Gnomad4 AMR exome

AF:

0.0392

Gnomad4 ASJ exome

AF:

0.0367

Gnomad4 EAS exome

AF:

0.0396

Gnomad4 SAS exome

AF:

0.0491

Gnomad4 FIN exome

AF:

0.0468

Gnomad4 NFE exome

AF:

0.0270

Gnomad4 OTH exome

AF:

0.0340

GnomAD4 genome

AF:

0.00101

AC:

AN:

89440

Hom.:

Cov.:

AF XY:

0.00170

AC XY:

AN XY:

41162

show subpopulations

Gnomad4 AFR

AF:

0.000260

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0322

Gnomad4 FIN

AF:

0.000340

Gnomad4 NFE

AF:

0.0000220

Gnomad4 OTH

AF:

0.000855

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 02, 2019

- -

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