rs3782851

Variant names:

• chr12-663292-C-T
• rs3782851
• NM_016533.6:c.33+36G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307
• Publications: 8 publications found

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

ACMG classification

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NINJ2	NM_016533.6	c.33+36G>A		intron_variant	Intron 1 of 3	ENST00000305108.10	NP_057617.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NINJ2	ENST00000305108.10	c.33+36G>A		intron_variant	Intron 1 of 3	1	NM_016533.6	ENSP00000307552.5
NINJ2	ENST00000662884.1	c.171+36G>A		intron_variant	Intron 1 of 3			ENSP00000499548.1
NINJ2-AS1	ENST00000543884.3	n.222-25C>T		intron_variant	Intron 2 of 2	3
NINJ2-AS1	ENST00000662519.1	n.453-25C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0615 AC: 9366 AN: 152182 Hom.: 431 Cov.: 33

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

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.: 27 AF XY: 0.0753 AC XY: 54098 AN XY: 718352

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

GnomAD4 genome AF: 0.0615 AC: 9368 AN: 152300 Hom.: 431 Cov.: 33 AF XY: 0.0660 AC XY: 4913 AN XY: 74476

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: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0612 AC: 4160 AN: 68022

Other (OTH) AF: 0.0676 AC: 143 AN: 2116

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.3
DANN	Benign	0.68
PhyloP100		0.31
PromoterAI		-0.076	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3782851; hg19: chr12-772458; COSMIC: COSV59324875;