rs34166160

Variant names:

• chr12-623339-C-A
• rs34166160
• NM_016533.6:c.33+39989G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-623339-C-A
• chr12-623339-C-G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_016533.6(NINJ2):​c.33+39989G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00846 in 152,290 control chromosomes in the GnomAD database, including 8 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 0.0085 (8 hom., cov: 32)
• Consequence: NINJ2 NM_016533.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470
• Publications: 4 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS2: High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NINJ2	NM_016533.6	c.33+39989G>T		intron_variant	Intron 1 of 3	ENST00000305108.10	NP_057617.3
NINJ2	NM_001294346.2	c.-76+20172G>T		intron_variant	Intron 1 of 3		NP_001281275.1
NINJ2	NM_001367996.1	c.-76+18021G>T		intron_variant	Intron 2 of 4		NP_001354925.1
NINJ2	NR_160428.1	n.126+20172G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NINJ2	ENST00000305108.10	c.33+39989G>T		intron_variant	Intron 1 of 3	1	NM_016533.6	ENSP00000307552.5

Frequencies

GnomAD3 genomes AF: 0.00848 AC: 1290 AN: 152172 Hom.: 8 Cov.: 32

Gnomad AFR AF: 0.00147

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.00452

Gnomad ASJ AF: 0.0210

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.0116

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.0105

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

GnomAD4 genome AF: 0.00846 AC: 1289 AN: 152290 Hom.: 8 Cov.: 32 AF XY: 0.00861 AC XY: 641 AN XY: 74478

African (AFR) AF: 0.00147 AC: 61 AN: 41566

American (AMR) AF: 0.00451 AC: 69 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0210 AC: 73 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00166 AC: 8 AN: 4830

European-Finnish (FIN) AF: 0.0116 AC: 123 AN: 10614

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0130 AC: 886 AN: 68006

Other (OTH) AF: 0.0104 AC: 22 AN: 2116

Alfa AF: 0.00850 Hom.: 1

Bravo AF: 0.00745

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.55
PhyloP100		-0.47
Mutation Taster		=100/0	polymorphism

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: rs34166160; hg19: chr12-732505;