chr12-631795-G-A

Variant names:

• chr12-631795-G-A
• rs10849373
• NM_016533.6:c.33+31533C>T

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+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
• 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)

ENSG00000256020 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NINJ2	NM_016533.6	MANE Select	c.33+31533C>T		intron	N/A	NP_057617.3
	NINJ2	NM_001294346.2		c.-76+11716C>T		intron	N/A	NP_001281275.1
	NINJ2	NM_001367996.1		c.-76+9565C>T		intron	N/A	NP_001354925.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NINJ2	ENST00000305108.10	TSL:1 MANE Select	c.33+31533C>T		intron	N/A	ENSP00000307552.5
	NINJ2	ENST00000662884.1		c.171+31533C>T		intron	N/A	ENSP00000499548.1
	NINJ2	ENST00000542920.1	TSL:2	c.-76+11716C>T		intron	N/A	ENSP00000438831.1

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

African (AFR) AF: 0.194 AC: 8059 AN: 41490

American (AMR) AF: 0.250 AC: 3814 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1095 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1097 AN: 5172

South Asian (SAS) AF: 0.198 AC: 952 AN: 4816

European-Finnish (FIN) AF: 0.270 AC: 2849 AN: 10570

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22669 AN: 67954

Other (OTH) AF: 0.299 AC: 629 AN: 2106

Alfa AF: 0.314 Hom.: 9723

Bravo AF: 0.270

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	3.0
DANN	Benign	0.80
PhyloP100		-0.46
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: rs10849373; hg19: chr12-740961;