dbSNP rs3736855: CNTRL:p.Val1398Val (chr9-121154742-T-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_007018.6(CNTRL):c.4194T>A(p.Val1398Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 1,597,718 control chromosomes in the GnomAD database, including 161,749 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 0.38 ( 12670 hom., cov: 32)

Exomes 𝑓: 0.45 ( 149079 hom. )

Consequence

CNTRL
NM_007018.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0860

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP7

Synonymous conserved (PhyloP=0.086 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTRL	NM_007018.6 link	c.4194T>A	p.Val1398Val	synonymous_variant	Exon 27 of 44	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.4194T>A	p.Val1398Val	synonymous_variant	Exon 27 of 44	5	NM_007018.6	ENSP00000362962.1		Q7Z7A1-1

Frequencies

GnomAD3 genomes

AF:

0.384

AC:

58319

AN:

151952

Hom.:

12658

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.600

Gnomad AMR

AF:

0.494

Gnomad ASJ

AF:

0.515

Gnomad EAS

AF:

0.553

Gnomad SAS

AF:

0.644

Gnomad FIN

AF:

0.487

Gnomad MID

AF:

0.465

Gnomad NFE

AF:

0.428

Gnomad OTH

AF:

0.418

GnomAD3 exomes

AF:

0.472

AC:

118174

AN:

250396

Hom.:

29548

AF XY:

0.484

AC XY:

65483

AN XY:

135386

show subpopulations

Gnomad AFR exome

AF:

0.166

Gnomad AMR exome

AF:

0.544

Gnomad ASJ exome

AF:

0.510

Gnomad EAS exome

AF:

0.553

Gnomad SAS exome

AF:

0.652

Gnomad FIN exome

AF:

0.465

Gnomad NFE exome

AF:

0.430

Gnomad OTH exome

AF:

0.466

GnomAD4 exome

AF:

0.447

AC:

645759

AN:

1445648

Hom.:

149079

Cov.:

AF XY:

0.454

AC XY:

326839

AN XY:

720184

show subpopulations

Gnomad4 AFR exome

AF:

0.164

Gnomad4 AMR exome

AF:

0.540

Gnomad4 ASJ exome

AF:

0.506

Gnomad4 EAS exome

AF:

0.529

Gnomad4 SAS exome

AF:

0.651

Gnomad4 FIN exome

AF:

0.462

Gnomad4 NFE exome

AF:

0.430

Gnomad4 OTH exome

AF:

0.445

GnomAD4 genome

AF:

0.384

AC:

58349

AN:

152070

Hom.:

12670

Cov.:

AF XY:

0.394

AC XY:

29270

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.175

Gnomad4 AMR

AF:

0.494

Gnomad4 ASJ

AF:

0.515

Gnomad4 EAS

AF:

0.554

Gnomad4 SAS

AF:

0.645

Gnomad4 FIN

AF:

0.487

Gnomad4 NFE

AF:

0.428

Gnomad4 OTH

AF:

0.418

Alfa

AF:

0.424

Hom.:

4667

Bravo

AF:

0.374

Asia WGS

AF:

0.541

AC:

1883

AN:

3478

EpiCase

AF:

0.440

EpiControl

AF:

0.434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

5.3

DANN

Benign

0.81

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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