rs4980959

Variant names:

• chr12-663507-C-A
• rs4980959
• ENST00000543884.3:n.412C>A

Your query was ambiguous. Multiple possible variants found:

• chr12-663507-C-A
• chr12-663507-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000543884.3(NINJ2-AS1):​n.412C>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 ENST00000543884.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259
• Publications: 18 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NINJ2	NM_016533.6	c.-147G>T		upstream_gene_variant		ENST00000305108.10	NP_057617.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NINJ2-AS1	ENST00000543884.3	n.412C>A		non_coding_transcript_exon_variant	Exon 3 of 3	3
NINJ2-AS1	ENST00000662519.1	n.643C>A		non_coding_transcript_exon_variant	Exon 3 of 3
NINJ2	ENST00000662884.1	c.-9G>T		5_prime_UTR_variant	Exon 1 of 4			ENSP00000499548.1
NINJ2	ENST00000305108.10	c.-147G>T		upstream_gene_variant		1	NM_016533.6	ENSP00000307552.5

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

GnomAD2 exomes AF: 0.382 AC: 85980 AN: 224972 AF XY: 0.379

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 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

African (AFR) AF: 0.342 AC: 11082 AN: 32438

American (AMR) AF: 0.376 AC: 14961 AN: 39826

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 8441 AN: 23930

East Asian (EAS) AF: 0.332 AC: 13096 AN: 39442

South Asian (SAS) AF: 0.338 AC: 27528 AN: 81498

European-Finnish (FIN) AF: 0.457 AC: 23696 AN: 51834

Middle Eastern (MID) AF: 0.304 AC: 1685 AN: 5538

European-Non Finnish (NFE) AF: 0.373 AC: 409479 AN: 1096398

Other (OTH) AF: 0.364 AC: 21480 AN: 58964

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

African (AFR) AF: 0.343 AC: 14224 AN: 41506

American (AMR) AF: 0.395 AC: 6042 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1222 AN: 3470

East Asian (EAS) AF: 0.356 AC: 1842 AN: 5174

South Asian (SAS) AF: 0.340 AC: 1642 AN: 4824

European-Finnish (FIN) AF: 0.453 AC: 4781 AN: 10562

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25915 AN: 67960

Other (OTH) AF: 0.375 AC: 792 AN: 2112

Alfa AF: 0.373 Hom.: 39893

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
PhyloP100		0.26
PromoterAI		-0.025	Neutral
Mutation Taster		=300/0	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: rs4980959; hg19: chr12-772673; COSMIC: COSV59323197;