NM_001382391.1:c.2122A>G

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001382391.1(CSPP1):c.2122A>G(p.Ser708Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000418 in 1,557,668 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S708R) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.00032 ( 2 hom., cov: 32)

Exomes 𝑓: 0.00043 ( 8 hom. )

Consequence

CSPP1
NM_001382391.1 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 6.87

Publications

4 publications found

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 Gene-Disease associations (from GenCC):

Joubert syndrome 21
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), G2P
Joubert syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Joubert syndrome with Jeune asphyxiating thoracic dystrophy
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Meckel syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

CSPP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0044882894).

BP6

Variant 8-67149929-A-G is Benign according to our data. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-67149929-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 541697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.000319 (48/150602) while in subpopulation SAS AF = 0.00987 (47/4764). AF 95% confidence interval is 0.00762. There are 2 homozygotes in GnomAd4. There are 31 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSPP1	NM_001382391.1 link	c.2122A>G	p.Ser708Gly	missense_variant	Exon 18 of 31	ENST00000678616.1	NP_001369320.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSPP1	ENST00000678616.1 link	c.2122A>G	p.Ser708Gly	missense_variant	Exon 18 of 31		NM_001382391.1	ENSP00000504733.1		A0A7I2V5W3

Frequencies

GnomAD3 genomes

AF:

0.000326

AC:

AN:

150494

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000244

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0101

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00101

AC:

196

AN:

193808

AF XY:

0.00119

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.000954

GnomAD4 exome

AF:

0.000429

AC:

603

AN:

1407066

Hom.:

Cov.:

AF XY:

0.000595

AC XY:

416

AN XY:

699284

show subpopulations

African (AFR)

AF:

0.0000332

AC:

AN:

30076

American (AMR)

AF:

0.00

AC:

AN:

29662

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

23346

East Asian (EAS)

AF:

0.00

AC:

AN:

38424

South Asian (SAS)

AF:

0.00732

AC:

556

AN:

75960

European-Finnish (FIN)

AF:

0.00

AC:

AN:

51736

Middle Eastern (MID)

AF:

0.000364

AC:

AN:

5496

European-Non Finnish (NFE)

AF:

0.00000183

AC:

AN:

1094624

Other (OTH)

AF:

0.000727

AC:

AN:

57742

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

116

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000319

AC:

AN:

150602

Hom.:

Cov.:

AF XY:

0.000422

AC XY:

AN XY:

73496

show subpopulations

African (AFR)

AF:

0.0000243

AC:

AN:

41090

American (AMR)

AF:

0.00

AC:

AN:

14902

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3464

East Asian (EAS)

AF:

0.00

AC:

AN:

5112

South Asian (SAS)

AF:

0.00987

AC:

AN:

4764

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10156

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

67834

Other (OTH)

AF:

0.00

AC:

AN:

2082

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000102

Hom.:

Bravo

AF:

0.0000680

ExAC

AF:

0.00115

AC:

139

Asia WGS

AF:

0.00202

AC:

AN:

3472

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Joubert syndrome 21

Benign:1

Dec 15, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Mar 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

CSPP1: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.56

CADD

Benign

(source)

DANN

Benign

0.97

Eigen

Benign

-0.12

Eigen_PC

Benign

0.14

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Benign

0.60

MetaRNN

Benign

0.0045

MetaSVM

Benign

-1.1

PhyloP100

6.9

PrimateAI

Benign

0.37

PROVEAN

Benign

-0.50

REVEL

Benign

0.027

Sift

Benign

0.50

Sift4G

Benign

0.37

Polyphen

0.0010

Vest4

0.34

MVP

0.29

MPC

0.11

ClinPred

0.080

GERP RS

6.0

gMVP

0.21

Mutation Taster

=97/3

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over