12-662511-G-C

Position:

• chr12-662511-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016533.6(NINJ2):​c.33+817C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,060 control chromosomes in the GnomAD database, including 3,575 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 0.22 (3575 hom., cov: 32)
• Consequence: NINJ2 NM_016533.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NINJ2	NM_016533.6	c.33+817C>G		intron_variant		ENST00000305108.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NINJ2	ENST00000305108.10	c.33+817C>G		intron_variant		1	NM_016533.6	P1
NINJ2-AS1	ENST00000543884.2	n.210-806G>C		intron_variant, non_coding_transcript_variant		3
NINJ2	ENST00000662884.1	c.171+817C>G		intron_variant
NINJ2-AS1	ENST00000662519.1	n.453-806G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32752 AN: 151942 Hom.: 3571 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.185

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.216 AC: 32780 AN: 152060 Hom.: 3575 Cov.: 32 AF XY: 0.221 AC XY: 16423 AN XY: 74330

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.185

Alfa AF: 0.211 Hom.: 433

Bravo AF: 0.211

Asia WGS AF: 0.210 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.58

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: rs11609955; hg19: chr12-771677;