12-587929-C-T

Variant names:

• chr12-587929-C-T
• rs11063749
• NM_016533.6:c.34-21751G>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.34-21751G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,016 control chromosomes in the GnomAD database, including 8,176 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 0.32 (8176 hom., cov: 32)
• Consequence: NINJ2 NM_016533.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.57
• Publications: 9 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]

ENSG00000256020 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NINJ2	NM_016533.6	c.34-21751G>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.34-21751G>A		intron_variant	Intron 1 of 3	1	NM_016533.6	ENSP00000307552.5

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49310 AN: 151898 Hom.: 8157 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.325 AC: 49371 AN: 152016 Hom.: 8176 Cov.: 32 AF XY: 0.328 AC XY: 24340 AN XY: 74290

African (AFR) AF: 0.378 AC: 15648 AN: 41434

American (AMR) AF: 0.405 AC: 6186 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1068 AN: 3470

East Asian (EAS) AF: 0.320 AC: 1655 AN: 5172

South Asian (SAS) AF: 0.374 AC: 1805 AN: 4826

European-Finnish (FIN) AF: 0.288 AC: 3044 AN: 10566

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18933 AN: 67964

Other (OTH) AF: 0.335 AC: 706 AN: 2108

Alfa AF: 0.298 Hom.: 8821

Bravo AF: 0.336

Asia WGS AF: 0.430 AC: 1490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.37
DANN	Benign	0.49
PhyloP100		-2.6
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: rs11063749; hg19: chr12-697095;