Variant 9-93125038-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004148.4(NINJ1):c.329C>A(p.Ala110Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 1,613,308 control chromosomes in the GnomAD database, including 524,719 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.77 ( 45896 hom., cov: 32)

Exomes 𝑓: 0.81 ( 478823 hom. )

Consequence

NINJ1
NM_004148.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.84

Variant links:

Genes affected

NINJ1 (HGNC:7824): (ninjurin 1) The ninjurin protein is upregulated after nerve injury both in dorsal root ganglion neurons and in Schwann cells (Araki and Milbrandt, 1996 [PubMed 8780658]). It demonstrates properties of a homophilic adhesion molecule and promotes neurite outgrowth from primary cultured dorsal root ganglion neurons.[supplied by OMIM, Aug 2009]

NINJ1 links:

NINJ1 (HGNC:):

NINJ1 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 (MetaRNN=9.656975E-7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NINJ1	NM_004148.4 linkuse as main transcript	c.329C>A	p.Ala110Asp	missense_variant	3/4	ENST00000375446.5	NP_004139.2	Q92982
NINJ1	XM_011518716.2 linkuse as main transcript	c.179C>A	p.Ala60Asp	missense_variant	4/5		XP_011517018.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
NINJ1	ENST00000375446.5 linkuse as main transcript	c.329C>A	p.Ala110Asp	missense_variant	3/4	1	NM_004148.4	ENSP00000364595.4	Q92982
NINJ1	ENST00000461162.5 linkuse as main transcript	n.388C>A		non_coding_transcript_exon_variant	4/5	2
NINJ1	ENST00000470314.5 linkuse as main transcript	n.297C>A		non_coding_transcript_exon_variant	3/4	3
NINJ1	ENST00000489274.1 linkuse as main transcript	n.1153C>A		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes

AF:

0.774

AC:

117560

AN:

151972

Hom.:

45855

Cov.:

show subpopulations

Gnomad AFR

AF:

0.671

Gnomad AMI

AF:

0.838

Gnomad AMR

AF:

0.838

Gnomad ASJ

AF:

0.791

Gnomad EAS

AF:

0.886

Gnomad SAS

AF:

0.829

Gnomad FIN

AF:

0.774

Gnomad MID

AF:

0.791

Gnomad NFE

AF:

0.807

Gnomad OTH

AF:

0.787

GnomAD3 exomes

AF:

0.810

AC:

203167

AN:

250742

Hom.:

82787

AF XY:

0.809

AC XY:

109626

AN XY:

135548

show subpopulations

Gnomad AFR exome

AF:

0.663

Gnomad AMR exome

AF:

0.890

Gnomad ASJ exome

AF:

0.788

Gnomad EAS exome

AF:

0.890

Gnomad SAS exome

AF:

0.819

Gnomad FIN exome

AF:

0.773

Gnomad NFE exome

AF:

0.801

Gnomad OTH exome

AF:

0.804

GnomAD4 exome

AF:

0.809

AC:

1182016

AN:

1461218

Hom.:

478823

Cov.:

AF XY:

0.809

AC XY:

587895

AN XY:

726910

show subpopulations

Gnomad4 AFR exome

AF:

0.665

Gnomad4 AMR exome

AF:

0.882

Gnomad4 ASJ exome

AF:

0.790

Gnomad4 EAS exome

AF:

0.859

Gnomad4 SAS exome

AF:

0.816

Gnomad4 FIN exome

AF:

0.775

Gnomad4 NFE exome

AF:

0.810

Gnomad4 OTH exome

AF:

0.801

GnomAD4 genome

AF:

0.774

AC:

117651

AN:

152090

Hom.:

45896

Cov.:

AF XY:

0.776

AC XY:

57671

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.671

Gnomad4 AMR

AF:

0.838

Gnomad4 ASJ

AF:

0.791

Gnomad4 EAS

AF:

0.886

Gnomad4 SAS

AF:

0.828

Gnomad4 FIN

AF:

0.774

Gnomad4 NFE

AF:

0.807

Gnomad4 OTH

AF:

0.789

Alfa

AF:

0.801

Hom.:

97840

Bravo

AF:

0.775

TwinsUK

AF:

0.801

AC:

2970

ALSPAC

AF:

0.818

AC:

3152

ESP6500AA

AF:

0.677

AC:

2981

ESP6500EA

AF:

0.814

AC:

7000

ExAC

AF:

0.804

AC:

97656

Asia WGS

AF:

0.854

AC:

2965

AN:

3478

EpiCase

AF:

0.802

EpiControl

AF:

0.806

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.65

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.14

Eigen

Benign

-0.12

Eigen_PC

Benign

-0.13

FATHMM_MKL

Uncertain

0.86

LIST_S2

Benign

0.45

MetaRNN

Benign

9.7e-7

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.0

PrimateAI

Uncertain

0.60

PROVEAN

Benign

-2.0

REVEL

Benign

0.15

Sift

Benign

0.54

Sift4G

Benign

0.52

Polyphen

0.94

Vest4

0.041

MPC

0.78

ClinPred

0.031

GERP RS

2.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

Varity_R

0.21

gMVP

0.91

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