Variant 14-50725941-G-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 ENST00000382041.7(NIN):c.6204C>T(p.Pro2068=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 1,613,432 control chromosomes in the GnomAD database, including 101,532 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 7244 hom., cov: 31)

Exomes 𝑓: 0.35 ( 94288 hom. )

Consequence

NIN
ENST00000382041.7 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.970

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 14-50725941-G-A is Benign according to our data. Variant chr14-50725941-G-A is described in ClinVar as [Benign]. Clinvar id is 1250757.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-50725941-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.97 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.366 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.6192+12C>T		intron_variant		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.6192+12C>T		intron_variant		5	NM_020921.4	ENSP00000436092	P2	Q8N4C6-7

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42399

AN:

151906

Hom.:

7245

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0825

Gnomad AMI

AF:

0.481

Gnomad AMR

AF:

0.257

Gnomad ASJ

AF:

0.306

Gnomad EAS

AF:

0.314

Gnomad SAS

AF:

0.381

Gnomad FIN

AF:

0.430

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.366

Gnomad OTH

AF:

0.289

GnomAD3 exomes

AF:

0.336

AC:

84340

AN:

251296

Hom.:

15257

AF XY:

0.344

AC XY:

46740

AN XY:

135808

show subpopulations

Gnomad AFR exome

AF:

0.0765

Gnomad AMR exome

AF:

0.280

Gnomad ASJ exome

AF:

0.314

Gnomad EAS exome

AF:

0.320

Gnomad SAS exome

AF:

0.379

Gnomad FIN exome

AF:

0.439

Gnomad NFE exome

AF:

0.363

Gnomad OTH exome

AF:

0.332

GnomAD4 exome

AF:

0.354

AC:

517802

AN:

1461408

Hom.:

94288

Cov.:

AF XY:

0.356

AC XY:

259079

AN XY:

727036

show subpopulations

Gnomad4 AFR exome

AF:

0.0699

Gnomad4 AMR exome

AF:

0.279

Gnomad4 ASJ exome

AF:

0.315

Gnomad4 EAS exome

AF:

0.290

Gnomad4 SAS exome

AF:

0.380

Gnomad4 FIN exome

AF:

0.445

Gnomad4 NFE exome

AF:

0.364

Gnomad4 OTH exome

AF:

0.336

GnomAD4 genome

AF:

0.279

AC:

42390

AN:

152024

Hom.:

7244

Cov.:

AF XY:

0.281

AC XY:

20856

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.0822

Gnomad4 AMR

AF:

0.257

Gnomad4 ASJ

AF:

0.306

Gnomad4 EAS

AF:

0.313

Gnomad4 SAS

AF:

0.381

Gnomad4 FIN

AF:

0.430

Gnomad4 NFE

AF:

0.366

Gnomad4 OTH

AF:

0.291

Alfa

AF:

0.331

Hom.:

7691

Bravo

AF:

0.258

Asia WGS

AF:

0.345

AC:

1200

AN:

3474

EpiCase

AF:

0.355

EpiControl

AF:

0.355

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	Aug 29, 2020	- -

Seckel syndrome 7

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.31

DANN

Benign

0.36

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