12-631795-G-A

Position:

• chr12-631795-G-A

Variant summary

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

The NM_016533.6(NINJ2):​c.33+31533C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,056 control chromosomes in the GnomAD database, including 6,158 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 0.27 (6158 hom., cov: 33)
• Consequence: NINJ2 NM_016533.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460

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=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NINJ2	NM_016533.6	c.33+31533C>T		intron_variant		ENST00000305108.10
NINJ2-AS1	NR_122124.1	n.96-419G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NINJ2	ENST00000305108.10	c.33+31533C>T		intron_variant		1	NM_016533.6	P1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41709 AN: 151938 Hom.: 6153 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.274 AC: 41723 AN: 152056 Hom.: 6158 Cov.: 33 AF XY: 0.269 AC XY: 20015 AN XY: 74324

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.299

Alfa AF: 0.321 Hom.: 7809

Bravo AF: 0.270

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	3.0
DANN	Benign	0.80

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: rs10849373; hg19: chr12-740961;