Variant 14-50757940-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_020921.4(NIN):c.3090A>T(p.Ser1030=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 1,613,906 control chromosomes in the GnomAD database, including 81,016 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.29 ( 7015 hom., cov: 32)

Exomes 𝑓: 0.31 ( 74001 hom. )

Consequence

NIN
NM_020921.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.919

Variant links:

Genes affected

NIN (HGNC:14906): (ninein) This gene encodes one of the proteins important for centrosomal function. This protein is important for positioning and anchoring the microtubules minus-ends in epithelial cells. Localization of this protein to the centrosome requires three leucine zippers in the central coiled-coil domain. Multiple alternatively spliced transcript variants that encode different isoforms have been reported. [provided by RefSeq, Jul 2008]

NIN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 14-50757940-T-A is Benign according to our data. Variant chr14-50757940-T-A is described in ClinVar as [Benign]. Clinvar id is 129786.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.919 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NIN	NM_020921.4 linkuse as main transcript	c.3090A>T	p.Ser1030=	synonymous_variant	18/31	ENST00000530997.7	NP_065972.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NIN	ENST00000530997.7 linkuse as main transcript	c.3090A>T	p.Ser1030=	synonymous_variant	18/31	5	NM_020921.4	ENSP00000436092	P2	Q8N4C6-7

Frequencies

GnomAD3 genomes

AF:

0.291

AC:

44258

AN:

151960

Hom.:

7003

Cov.:

show subpopulations

Gnomad AFR

AF:

0.194

Gnomad AMI

AF:

0.206

Gnomad AMR

AF:

0.405

Gnomad ASJ

AF:

0.355

Gnomad EAS

AF:

0.504

Gnomad SAS

AF:

0.241

Gnomad FIN

AF:

0.310

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.307

Gnomad OTH

AF:

0.292

GnomAD3 exomes

AF:

0.336

AC:

84602

AN:

251454

Hom.:

15437

AF XY:

0.328

AC XY:

44618

AN XY:

135904

show subpopulations

Gnomad AFR exome

AF:

0.189

Gnomad AMR exome

AF:

0.499

Gnomad ASJ exome

AF:

0.360

Gnomad EAS exome

AF:

0.510

Gnomad SAS exome

AF:

0.245

Gnomad FIN exome

AF:

0.309

Gnomad NFE exome

AF:

0.308

Gnomad OTH exome

AF:

0.324

GnomAD4 exome

AF:

0.314

AC:

458335

AN:

1461828

Hom.:

74001

Cov.:

AF XY:

0.310

AC XY:

225706

AN XY:

727224

show subpopulations

Gnomad4 AFR exome

AF:

0.185

Gnomad4 AMR exome

AF:

0.485

Gnomad4 ASJ exome

AF:

0.358

Gnomad4 EAS exome

AF:

0.496

Gnomad4 SAS exome

AF:

0.244

Gnomad4 FIN exome

AF:

0.303

Gnomad4 NFE exome

AF:

0.309

Gnomad4 OTH exome

AF:

0.316

GnomAD4 genome

AF:

0.291

AC:

44283

AN:

152078

Hom.:

7015

Cov.:

AF XY:

0.295

AC XY:

21940

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.194

Gnomad4 AMR

AF:

0.406

Gnomad4 ASJ

AF:

0.355

Gnomad4 EAS

AF:

0.505

Gnomad4 SAS

AF:

0.241

Gnomad4 FIN

AF:

0.310

Gnomad4 NFE

AF:

0.307

Gnomad4 OTH

AF:

0.289

Alfa

AF:

0.269

Hom.:

1840

Bravo

AF:

0.299

Asia WGS

AF:

0.316

AC:

1100

AN:

3478

EpiCase

AF:

0.310

EpiControl

AF:

0.309

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

not specified

Benign:1

Likely benign, no assertion criteria provided

clinical testing

Genetic Services Laboratory, University of Chicago

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.57

DANN

Benign

0.54

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over