dbSNP rs3747843: CNTRL:c.3964-457A>G (chr9-121152028-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_007018.6(CNTRL):c.3964-457A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 156,908 control chromosomes in the GnomAD database, including 18,260 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 0.45 ( 17478 hom., cov: 32)

Exomes 𝑓: 0.54 ( 782 hom. )

Consequence

CNTRL
NM_007018.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0520

Publications

6 publications found

Variant links:

Genes affected

CNTRL (HGNC:1858): (centriolin) This gene encodes a centrosomal protein required for the centrosome to function as a microtubule organizing center. The gene product is also associated with centrosome maturation. One version of stem cell myeloproliferative disorder is the result of a reciprocal translocation between chromosomes 8 and 9, with the breakpoint associated with fibroblast growth factor receptor 1 and centrosomal protein 1. [provided by RefSeq, Jul 2008]

CNTRL 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTRL	NM_007018.6 link	c.3964-457A>G		intron_variant	Intron 25 of 43	ENST00000373855.7	NP_008949.4	Q7Z7A1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTRL	ENST00000373855.7 link	c.3964-457A>G		intron_variant	Intron 25 of 43	5	NM_007018.6	ENSP00000362962.1		Q7Z7A1-1

Frequencies

GnomAD3 genomes

AF:

0.452

AC:

68703

AN:

152018

Hom.:

17464

Cov.:

show subpopulations

Gnomad AFR

AF:

0.227

Gnomad AMI

AF:

0.657

Gnomad AMR

AF:

0.609

Gnomad ASJ

AF:

0.552

Gnomad EAS

AF:

0.738

Gnomad SAS

AF:

0.781

Gnomad FIN

AF:

0.553

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.484

Gnomad OTH

AF:

0.478

GnomAD4 exome

AF:

0.539

AC:

2572

AN:

4772

Hom.:

782

Cov.:

AF XY:

0.536

AC XY:

1332

AN XY:

2486

show subpopulations

African (AFR)

AF:

0.222

AC:

AN:

American (AMR)

AF:

0.652

AC:

668

AN:

1024

Ashkenazi Jewish (ASJ)

AF:

0.385

AC:

AN:

East Asian (EAS)

AF:

0.730

AC:

149

AN:

204

South Asian (SAS)

AF:

0.751

AC:

401

AN:

534

European-Finnish (FIN)

AF:

0.438

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.453

AC:

1227

AN:

2706

Other (OTH)

AF:

0.488

AC:

AN:

172

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

140

187

234

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

168

210

<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:

0.452

AC:

68752

AN:

152136

Hom.:

17478

Cov.:

AF XY:

0.466

AC XY:

34621

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.227

AC:

9428

AN:

41506

American (AMR)

AF:

0.610

AC:

9317

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.552

AC:

1916

AN:

3470

East Asian (EAS)

AF:

0.739

AC:

3829

AN:

5184

South Asian (SAS)

AF:

0.781

AC:

3776

AN:

4834

European-Finnish (FIN)

AF:

0.553

AC:

5848

AN:

10572

Middle Eastern (MID)

AF:

0.500

AC:

147

AN:

294

European-Non Finnish (NFE)

AF:

0.484

AC:

32881

AN:

67974

Other (OTH)

AF:

0.480

AC:

1013

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1781

3561

5342

7122

8903

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

628

1256

1884

2512

3140

<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:

0.477

Hom.:

23381

Bravo

AF:

0.444

Asia WGS

AF:

0.686

AC:

2383

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.0

(source)

DANN

Benign

0.61

PhyloP100

-0.052

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