8-67149947-CTTTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTT

Position:

• chr8-67149947-CTTTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_001382391.1(CSPP1):​c.2128+36dupT 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 0.00049 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0057 (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 Likely_benign. Variant got -4 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.00569 (5936/1042846) while in subpopulation SAS AF= 0.00757 (325/42936). AF 95% confidence interval is 0.00689. There are 0 homozygotes in gnomad4_exome. There are 2900 alleles in male gnomad4_exome 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	c.2128+36dupT		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+36dupT		intron_variant			NM_001382391.1	ENSP00000504733.1

Frequencies

GnomAD3 genomes AF: 0.000492 AC: 44 AN: 89384 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000520

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.000407

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.00119

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.000508

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00324 AC: 217 AN: 66916 Hom.: 0 AF XY: 0.00298 AC XY: 108 AN XY: 36278

Gnomad AFR exome AF: 0.00439

Gnomad AMR exome AF: 0.00356

Gnomad ASJ exome AF: 0.00174

Gnomad EAS exome AF: 0.00575

Gnomad SAS exome AF: 0.00309

Gnomad FIN exome AF: 0.00194

Gnomad NFE exome AF: 0.00300

Gnomad OTH exome AF: 0.00351

GnomAD4 exome AF: 0.00569 AC: 5936 AN: 1042846 Hom.: 0 Cov.: 0 AF XY: 0.00564 AC XY: 2900 AN XY: 514582

Gnomad4 AFR exome AF: 0.00473

Gnomad4 AMR exome AF: 0.00429

Gnomad4 ASJ exome AF: 0.00478

Gnomad4 EAS exome AF: 0.00640

Gnomad4 SAS exome AF: 0.00757

Gnomad4 FIN exome AF: 0.00376

Gnomad4 NFE exome AF: 0.00569

Gnomad4 OTH exome AF: 0.00629

GnomAD4 genome AF: 0.000492 AC: 44 AN: 89354 Hom.: 0 Cov.: 0 AF XY: 0.000535 AC XY: 22 AN XY: 41118

Gnomad4 AFR AF: 0.000520

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.000407

Gnomad4 EAS AF: 0.000968

Gnomad4 SAS AF: 0.00119

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000508

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs11296619; hg19: chr8-68062182;