Variant 1-184795276-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_052966.4(NIBAN1):c.2488G>A(p.Gly830Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00678 in 1,612,926 control chromosomes in the GnomAD database, including 265 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.024 ( 105 hom., cov: 33)

Exomes 𝑓: 0.0050 ( 160 hom. )

Consequence

NIBAN1
NM_052966.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.163

Variant links:

Genes affected

NIBAN1 (HGNC:16784): (niban apoptosis regulator 1) This gene encodes a member of the family with sequence similarity 129 protein family. This gene is highly expressed in several cancer cells and may serve as a prognostic marker for certain cancers. The encoded protein may play a role in regulating p53-mediated apoptosis. [provided by RefSeq, Sep 2016]

NIBAN1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.002091676).

BP6

Variant 1-184795276-C-T is Benign according to our data. Variant chr1-184795276-C-T is described in ClinVar as [Benign]. Clinvar id is 780286.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NIBAN1	NM_052966.4 link	c.2488G>A	p.Gly830Ser	missense_variant	14/14	ENST00000367511.4	NP_443198.1	Q9BZQ8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
NIBAN1	ENST00000367511.4 link	c.2488G>A	p.Gly830Ser	missense_variant	14/14	1	NM_052966.4	ENSP00000356481.3	Q9BZQ8
NIBAN1	ENST00000417056.5 link	c.259+2803G>A		intron_variant		3		ENSP00000414039.1	H0Y7M9
NIBAN1	ENST00000487074.5 link	n.1960G>A		non_coding_transcript_exon_variant	9/9	5

Frequencies

GnomAD3 genomes

AF:

0.0235

AC:

3578

AN:

152216

Hom.:

106

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0723

Gnomad AMI

AF:

0.0186

Gnomad AMR

AF:

0.0139

Gnomad ASJ

AF:

0.00749

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.00372

Gnomad OTH

AF:

0.0253

GnomAD3 exomes

AF:

0.00839

AC:

2098

AN:

250050

Hom.:

AF XY:

0.00642

AC XY:

868

AN XY:

135304

show subpopulations

Gnomad AFR exome

AF:

0.0754

Gnomad AMR exome

AF:

0.00954

Gnomad ASJ exome

AF:

0.00904

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000425

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00334

Gnomad OTH exome

AF:

0.0101

GnomAD4 exome

AF:

0.00503

AC:

7344

AN:

1460592

Hom.:

160

Cov.:

AF XY:

0.00472

AC XY:

3429

AN XY:

726656

show subpopulations

Gnomad4 AFR exome

AF:

0.0787

Gnomad4 AMR exome

AF:

0.0104

Gnomad4 ASJ exome

AF:

0.00899

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000846

Gnomad4 FIN exome

AF:

0.0000192

Gnomad4 NFE exome

AF:

0.00278

Gnomad4 OTH exome

AF:

0.0109

GnomAD4 genome

AF:

0.0235

AC:

3586

AN:

152334

Hom.:

105

Cov.:

AF XY:

0.0229

AC XY:

1705

AN XY:

74498

show subpopulations

Gnomad4 AFR

AF:

0.0724

Gnomad4 AMR

AF:

0.0139

Gnomad4 ASJ

AF:

0.00749

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000827

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00370

Gnomad4 OTH

AF:

0.0251

Alfa

AF:

0.0129

Hom.:

Bravo

AF:

0.0277

TwinsUK

AF:

0.00216

AC:

ALSPAC

AF:

0.00337

AC:

ESP6500AA

AF:

0.0699

AC:

308

ESP6500EA

AF:

0.00407

AC:

ExAC

AF:

0.00924

AC:

1122

Asia WGS

AF:

0.00520

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.074

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.81

CADD

Benign

5.4

DANN

Benign

0.65

DEOGEN2

Benign

0.022

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.025

LIST_S2

Benign

0.37

MetaRNN

Benign

0.0021

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.1

PrimateAI

Benign

0.21

PROVEAN

Benign

0.12

REVEL

Benign

0.029

Sift

Benign

0.25

Sift4G

Benign

0.42

Polyphen

0.058

Vest4

0.049

MVP

0.072

MPC

0.075

ClinPred

0.0026

GERP RS

-2.0

Varity_R

0.091

gMVP

0.086

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