rs12229103

chr12-592351-C-A

Variant summary

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

The NM_016533.6(NINJ2):c.34-26173G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0925 in 152,130 control chromosomes in the GnomAD database, including 892 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 0.093 (892 hom., cov: 32)
• Consequence: NINJ2 NM_016533.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NINJ2	NM_016533.6	c.34-26173G>T		intron_variant		ENST00000305108.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NINJ2	ENST00000305108.10	c.34-26173G>T		intron_variant		1	NM_016533.6	P1

Frequencies

GnomAD3 genomes AF: 0.0924 AC: 14048 AN: 152012 Hom.: 890 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0570

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.00905

Gnomad SAS AF: 0.00684

Gnomad FIN AF: 0.0830

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.0733

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

GnomAD4 genome AF: 0.0925 AC: 14077 AN: 152130 Hom.: 892 Cov.: 32 AF XY: 0.0897 AC XY: 6667 AN XY: 74364

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.0568

Gnomad4 ASJ AF: 0.0115

Gnomad4 EAS AF: 0.00907

Gnomad4 SAS AF: 0.00663

Gnomad4 FIN AF: 0.0830

Gnomad4 NFE AF: 0.0640

Gnomad4 OTH AF: 0.0725

Alfa AF: 0.0625 Hom.: 736

Bravo AF: 0.0954

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.5
Dann	Benign	0.70

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: rs12229103; hg19: chr12-701517;