8-67149947-CTTTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTT

Position:

• chr8-67149947-CTTTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001382391.1(CSPP1):​c.2128+28_2128+36dupTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00029 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000011 (0 hom.)
• Consequence: CSPP1 NM_001382391.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

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 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSPP1	NM_001382391.1	c.2128+28_2128+36dupTTTTTTTTT		intron_variant		ENST00000678616.1	NP_001369320.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSPP1	ENST00000678616.1	c.2128+28_2128+36dupTTTTTTTTT		intron_variant			NM_001382391.1	ENSP00000504733.1

Frequencies

GnomAD3 genomes AF: 0.000291 AC: 26 AN: 89336 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000174

Gnomad AMI AF: 0.00334

Gnomad AMR AF: 0.000249

Gnomad ASJ AF: 0.000407

Gnomad EAS AF: 0.000321

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000340

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000309

Gnomad OTH AF: 0.000858

GnomAD4 exome AF: 0.0000114 AC: 12 AN: 1049682 Hom.: 0 Cov.: 0 AF XY: 0.0000193 AC XY: 10 AN XY: 517920

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000684

Gnomad4 SAS exome AF: 0.000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000596

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.000291 AC: 26 AN: 89308 Hom.: 0 Cov.: 0 AF XY: 0.000146 AC XY: 6 AN XY: 41112

Gnomad4 AFR AF: 0.000173

Gnomad4 AMR AF: 0.000249

Gnomad4 ASJ AF: 0.000407

Gnomad4 EAS AF: 0.000323

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000340

Gnomad4 NFE AF: 0.000309

Gnomad4 OTH AF: 0.000855

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11296619; hg19: chr8-68062182;