dbSNP rs3782851: NINJ2:c.33+36G>A (chr12-663292-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016533.6(NINJ2):c.33+36G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.072 in 1,594,584 control chromosomes in the GnomAD database, including 5,445 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 0.062 ( 431 hom., cov: 33)

Exomes 𝑓: 0.073 ( 5014 hom. )

Consequence

NINJ2
NM_016533.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.307

Publications

8 publications found

Variant links:

Genes affected

NINJ2 (HGNC:7825): (ninjurin 2) The protein encoded by this gene belongs to the ninjurin (for nerve injury induced) family. It is a cell surface adhesion protein that is upregulated in Schwann cells surrounding the distal segment of injured nerve, and promotes neurite outgrowth, thus may have a role in nerve regeneration after nerve injury. [provided by RefSeq, Oct 2011]

NINJ2 links:

NINJ2-AS1 (HGNC:40405): (NINJ2 antisense RNA 1)

NINJ2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016533.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NINJ2	NM_016533.6	MANE Select	c.33+36G>A		intron	N/A	NP_057617.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NINJ2	ENST00000305108.10	TSL:1 MANE Select	c.33+36G>A	intron	N/A	ENSP00000307552.5	Q9NZG7
NINJ2	ENST00000662884.1		c.171+36G>A	intron	N/A	ENSP00000499548.1	A0A590UJR9
NINJ2	ENST00000857849.1		c.33+36G>A	intron	N/A	ENSP00000527908.1

Frequencies

GnomAD3 genomes

AF:

0.0615

AC:

9366

AN:

152182

Hom.:

431

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0144

Gnomad AMI

AF:

0.0363

Gnomad AMR

AF:

0.112

Gnomad ASJ

AF:

0.0591

Gnomad EAS

AF:

0.186

Gnomad SAS

AF:

0.148

Gnomad FIN

AF:

0.0764

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0612

Gnomad OTH

AF:

0.0683

GnomAD2 exomes

AF:

0.0979

AC:

23847

AN:

243500

AF XY:

0.0983

show subpopulations

Gnomad AFR exome

AF:

0.0134

Gnomad AMR exome

AF:

0.187

Gnomad ASJ exome

AF:

0.0643

Gnomad EAS exome

AF:

0.184

Gnomad FIN exome

AF:

0.0774

Gnomad NFE exome

AF:

0.0625

Gnomad OTH exome

AF:

0.0845

GnomAD4 exome

AF:

0.0731

AC:

105475

AN:

1442284

Hom.:

5014

Cov.:

AF XY:

0.0753

AC XY:

54098

AN XY:

718352

show subpopulations

African (AFR)

AF:

0.0105

AC:

346

AN:

32966

American (AMR)

AF:

0.175

AC:

7601

AN:

43404

Ashkenazi Jewish (ASJ)

AF:

0.0621

AC:

1588

AN:

25580

East Asian (EAS)

AF:

0.181

AC:

7170

AN:

39552

South Asian (SAS)

AF:

0.151

AC:

12852

AN:

85250

European-Finnish (FIN)

AF:

0.0787

AC:

4120

AN:

52332

Middle Eastern (MID)

AF:

0.0858

AC:

491

AN:

5724

European-Non Finnish (NFE)

AF:

0.0610

AC:

66970

AN:

1097784

Other (OTH)

AF:

0.0727

AC:

4337

AN:

59692

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

4893

9787

14680

19574

24467

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2650

5300

7950

10600

13250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0615

AC:

9368

AN:

152300

Hom.:

431

Cov.:

AF XY:

0.0660

AC XY:

4913

AN XY:

74476

show subpopulations

African (AFR)

AF:

0.0144

AC:

597

AN:

41580

American (AMR)

AF:

0.112

AC:

1711

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0591

AC:

205

AN:

3466

East Asian (EAS)

AF:

0.186

AC:

964

AN:

5174

South Asian (SAS)

AF:

0.149

AC:

719

AN:

4828

European-Finnish (FIN)

AF:

0.0764

AC:

811

AN:

10616

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0612

AC:

4160

AN:

68022

Other (OTH)

AF:

0.0676

AC:

143

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

439

878

1318

1757

2196

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

240

360

480

600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0614

Hom.:

372

Bravo

AF:

0.0625

Asia WGS

AF:

0.141

AC:

489

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.3

(source)

DANN

Benign

0.68

PhyloP100

0.31

PromoterAI

-0.076

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over