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

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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

Gnomad4 AFR exome

AF:

0.222

Gnomad4 AMR exome

AF:

0.652

Gnomad4 ASJ exome

AF:

0.385

Gnomad4 EAS exome

AF:

0.730

Gnomad4 SAS exome

AF:

0.751

Gnomad4 FIN exome

AF:

0.438

Gnomad4 NFE exome

AF:

0.453

Gnomad4 OTH exome

AF:

0.488

GnomAD4 genome

AF:

0.452

AC:

68752

AN:

152136

Hom.:

17478

Cov.:

AF XY:

0.466

AC XY:

34621

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.227

Gnomad4 AMR

AF:

0.610

Gnomad4 ASJ

AF:

0.552

Gnomad4 EAS

AF:

0.739

Gnomad4 SAS

AF:

0.781

Gnomad4 FIN

AF:

0.553

Gnomad4 NFE

AF:

0.484

Gnomad4 OTH

AF:

0.480

Alfa

AF:

0.485

Hom.:

18246

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

DANN

Benign

0.61

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over