chr12-664290-C-T

Variant names:

• chr12-664290-C-T
• rs3809263
• ENST00000543884.3:n.*145C>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.*145C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,338 control chromosomes in the GnomAD database, including 8,887 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 0.33 (8887 hom., cov: 30)
• Consequence: NINJ2-AS1 ENST00000543884.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 16 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NINJ2-AS1	ENST00000543884.3	n.*145C>T		downstream_gene_variant		3
NINJ2-AS1	ENST00000662519.1	n.*94C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50197 AN: 151220 Hom.: 8882 Cov.: 30

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.332 AC: 50221 AN: 151338 Hom.: 8887 Cov.: 30 AF XY: 0.335 AC XY: 24754 AN XY: 73854

African (AFR) AF: 0.198 AC: 8146 AN: 41224

American (AMR) AF: 0.379 AC: 5749 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1209 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1833 AN: 5164

South Asian (SAS) AF: 0.341 AC: 1636 AN: 4798

European-Finnish (FIN) AF: 0.455 AC: 4728 AN: 10392

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25808 AN: 67810

Other (OTH) AF: 0.339 AC: 713 AN: 2102

Alfa AF: 0.364 Hom.: 11008

Bravo AF: 0.322

Asia WGS AF: 0.394 AC: 1372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.47
PhyloP100		0.013

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3809263; hg19: chr12-773456;