8-67149947-CTTTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTT

Position:

• chr8-67149947-CTTTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTT

Variant summary

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

The NM_001382391.1(CSPP1):​c.2128+35_2128+36dupTT 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 0.00055 (1 hom., cov: 0)
  • Exomes 𝑓: 0.00067 (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 = 0.000667 (699/1047700) while in subpopulation SAS AF= 0.00139 (60/43082). AF 95% confidence interval is 0.00111. There are 0 homozygotes in gnomad4_exome. There are 360 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+35_2128+36dupTT		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+35_2128+36dupTT		intron_variant			NM_001382391.1	ENSP00000504733.1

Frequencies

GnomAD3 genomes AF: 0.000548 AC: 49 AN: 89468 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.000173

Gnomad AMI AF: 0.00167

Gnomad AMR AF: 0.000872

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000749

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000667 AC: 699 AN: 1047700 Hom.: 0 Cov.: 0 AF XY: 0.000696 AC XY: 360 AN XY: 516912

Gnomad4 AFR exome AF: 0.000453

Gnomad4 AMR exome AF: 0.00111

Gnomad4 ASJ exome AF: 0.000130

Gnomad4 EAS exome AF: 0.000787

Gnomad4 SAS exome AF: 0.00139

Gnomad4 FIN exome AF: 0.000442

Gnomad4 NFE exome AF: 0.000650

Gnomad4 OTH exome AF: 0.000512

GnomAD4 genome AF: 0.000548 AC: 49 AN: 89440 Hom.: 1 Cov.: 0 AF XY: 0.000705 AC XY: 29 AN XY: 41162

Gnomad4 AFR AF: 0.000173

Gnomad4 AMR AF: 0.000872

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000968

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000749

Gnomad4 OTH AF: 0.00

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;