rs4980959

chr12-663507-C-Achr12-663507-C-T

Variant summary

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

The ENST00000543884.2(NINJ2-AS1):n.400C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 1,581,966 control chromosomes in the GnomAD database, including 110,007 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 0.37 (10654 hom., cov: 33)
  • Exomes 𝑓: 0.37 (99353 hom.)
• Consequence: NINJ2-AS1 ENST00000543884.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259

Genes affected

NINJ2-AS1 (HGNC:40405): (NINJ2 antisense RNA 1)

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NINJ2-AS1	ENST00000543884.2	n.400C>A		non_coding_transcript_exon_variant	3/3	3
NINJ2	ENST00000662884.1	c.-9G>T		5_prime_UTR_variant	1/4
NINJ2-AS1	ENST00000662519.1	n.643C>A		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56806 AN: 151978 Hom.: 10642 Cov.: 33

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.371

GnomAD3 exomes AF: 0.382 AC: 85980 AN: 224972 Hom.: 16734 AF XY: 0.379 AC XY: 45904 AN XY: 120972

Gnomad AFR exome AF: 0.352

Gnomad AMR exome AF: 0.371

Gnomad ASJ exome AF: 0.351

Gnomad EAS exome AF: 0.377

Gnomad SAS exome AF: 0.345

Gnomad FIN exome AF: 0.460

Gnomad NFE exome AF: 0.388

Gnomad OTH exome AF: 0.385

GnomAD4 exome AF: 0.372 AC: 531448 AN: 1429868 Hom.: 99353 Cov.: 35 AF XY: 0.370 AC XY: 262389 AN XY: 708816

Gnomad4 AFR exome AF: 0.342

Gnomad4 AMR exome AF: 0.376

Gnomad4 ASJ exome AF: 0.353

Gnomad4 EAS exome AF: 0.332

Gnomad4 SAS exome AF: 0.338

Gnomad4 FIN exome AF: 0.457

Gnomad4 NFE exome AF: 0.373

Gnomad4 OTH exome AF: 0.364

GnomAD4 genome AF: 0.374 AC: 56863 AN: 152098 Hom.: 10654 Cov.: 33 AF XY: 0.375 AC XY: 27904 AN XY: 74346

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.375

Alfa AF: 0.369 Hom.: 18374

Bravo AF: 0.371

Asia WGS AF: 0.402 AC: 1400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	10
Dann	Benign	0.73

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: rs4980959; hg19: chr12-772673; COSMIC: COSV59323197;