Genetic Variant CSTPP1:c.366-722C>T (chr11-47154454-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024113.5(CSTPP1):c.366-722C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,036 control chromosomes in the GnomAD database, including 9,294 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.34 ( 9288 hom., cov: 32)

Exomes 𝑓: 0.29 ( 6 hom. )

Consequence

CSTPP1
NM_024113.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.470

Publications

27 publications found

Variant links:

Genes affected

CSTPP1 (HGNC:28720): (centriolar satellite-associated tubulin polyglutamylase complex regulator 1)

CSTPP1 links:

LOC124902672 (HGNC:):

LOC124902672 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSTPP1	NM_024113.5 link	c.366-722C>T		intron_variant	Intron 4 of 8	ENST00000278460.12	NP_077018.1	Q9H6J7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSTPP1	ENST00000278460.12 link	c.366-722C>T		intron_variant	Intron 4 of 8	1	NM_024113.5	ENSP00000278460.8		Q9H6J7-1

Frequencies

GnomAD3 genomes

AF:

0.340

AC:

51647

AN:

151796

Hom.:

9269

Cov.:

show subpopulations

Gnomad AFR

AF:

0.298

Gnomad AMI

AF:

0.306

Gnomad AMR

AF:

0.371

Gnomad ASJ

AF:

0.269

Gnomad EAS

AF:

0.704

Gnomad SAS

AF:

0.335

Gnomad FIN

AF:

0.417

Gnomad MID

AF:

0.283

Gnomad NFE

AF:

0.325

Gnomad OTH

AF:

0.311

GnomAD4 exome

AF:

0.287

AC:

AN:

122

Hom.:

Cov.:

AF XY:

0.292

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.563

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.245

AC:

AN:

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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

GnomAD4 genome

AF:

0.340

AC:

51711

AN:

151914

Hom.:

9288

Cov.:

AF XY:

0.347

AC XY:

25781

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.299

AC:

12385

AN:

41410

American (AMR)

AF:

0.371

AC:

5669

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.269

AC:

932

AN:

3468

East Asian (EAS)

AF:

0.706

AC:

3634

AN:

5150

South Asian (SAS)

AF:

0.335

AC:

1613

AN:

4814

European-Finnish (FIN)

AF:

0.417

AC:

4390

AN:

10534

Middle Eastern (MID)

AF:

0.288

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.325

AC:

22080

AN:

67954

Other (OTH)

AF:

0.305

AC:

645

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1707

3414

5122

6829

8536

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

524

1048

1572

2096

2620

<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:

0.323

Hom.:

21909

Bravo

AF:

0.339

Asia WGS

AF:

0.434

AC:

1504

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.4

(source)

DANN

Benign

0.80

PhyloP100

-0.47

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over