rs3782851

Positions:

• chr12-663292-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
NINJ2	NM_016533.6	c.33+36G>A		intron_variant		ENST00000305108.10	NP_057617.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NINJ2	ENST00000305108.10	c.33+36G>A		intron_variant		1	NM_016533.6	ENSP00000307552	P1
NINJ2-AS1	ENST00000543884.2	n.210-25C>T		intron_variant, non_coding_transcript_variant		3
NINJ2	ENST00000662884.1	c.171+36G>A		intron_variant				ENSP00000499548
NINJ2-AS1	ENST00000662519.1	n.453-25C>T		intron_variant, non_coding_transcript_variant

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

GnomAD3 exomes AF: 0.0979 AC: 23847 AN: 243500 Hom.: 1663 AF XY: 0.0983 AC XY: 12968 AN XY: 131928

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 SAS exome AF: 0.150

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

Gnomad4 AFR exome AF: 0.0105

Gnomad4 AMR exome AF: 0.175

Gnomad4 ASJ exome AF: 0.0621

Gnomad4 EAS exome AF: 0.181

Gnomad4 SAS exome AF: 0.151

Gnomad4 FIN exome AF: 0.0787

Gnomad4 NFE exome AF: 0.0610

Gnomad4 OTH exome AF: 0.0727

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

Gnomad4 AFR AF: 0.0144

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0591

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0764

Gnomad4 NFE AF: 0.0612

Gnomad4 OTH AF: 0.0676

Alfa AF: 0.0671 Hom.: 240

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

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

Other links and lift over

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