12-591509-G-C

Variant names:

• chr12-591509-G-C
• rs2607924
• NM_016533.6:c.34-25331C>G

Variant summary

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

The NM_016533.6(NINJ2):​c.34-25331C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 152,052 control chromosomes in the GnomAD database, including 43,581 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 0.76 (43581 hom., cov: 31)
• Consequence: NINJ2 NM_016533.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NINJ2	NM_016533.6	c.34-25331C>G		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.34-25331C>G		intron_variant	Intron 1 of 3	1	NM_016533.6	ENSP00000307552.5

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114848 AN: 151934 Hom.: 43534 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.756 AC: 114956 AN: 152052 Hom.: 43581 Cov.: 31 AF XY: 0.751 AC XY: 55783 AN XY: 74308

African (AFR) AF: 0.750 AC: 31085 AN: 41460

American (AMR) AF: 0.772 AC: 11794 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2687 AN: 3472

East Asian (EAS) AF: 0.546 AC: 2826 AN: 5172

South Asian (SAS) AF: 0.699 AC: 3367 AN: 4820

European-Finnish (FIN) AF: 0.742 AC: 7837 AN: 10564

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.776 AC: 52754 AN: 67972

Other (OTH) AF: 0.773 AC: 1635 AN: 2116

Alfa AF: 0.698 Hom.: 2043

Bravo AF: 0.760

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.26
DANN	Benign	0.49
PhyloP100		-2.4
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: rs2607924; hg19: chr12-700675;