rs2972090

Variant names:

• chr2-55042252-A-C
• rs2972090
• NM_020532.5:c.556+7493T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-55042252-A-C
• chr2-55042252-A-T

Variant summary

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

The NM_020532.5(RTN4):​c.556+7493T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 151,930 control chromosomes in the GnomAD database, including 33,982 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 0.67 (33982 hom., cov: 32)
• Consequence: RTN4 NM_020532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311
• Publications: 1 publications found

Genes affected

RTN4 (HGNC:14085): (reticulon 4) This gene belongs to the family of reticulon encoding genes. Reticulons are associated with the endoplasmic reticulum, and are involved in neuroendocrine secretion or in membrane trafficking in neuroendocrine cells. The product of this gene is a potent neurite outgrowth inhibitor which may also help block the regeneration of the central nervous system in higher vertebrates. Alternatively spliced transcript variants derived both from differential splicing and differential promoter usage and encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020532.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RTN4	NM_020532.5	MANE Select	c.556+7493T>G		intron	N/A	NP_065393.1	Q9NQC3-1
	RTN4	NM_001321859.2		c.-63+8465T>G		intron	N/A	NP_001308788.1	Q9NQC3-6
	RTN4	NM_001321860.1		c.-63+8176T>G		intron	N/A	NP_001308789.1	Q9NQC3-6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RTN4	ENST00000337526.11	TSL:1 MANE Select	c.556+7493T>G		intron	N/A	ENSP00000337838.6	Q9NQC3-1
	RTN4	ENST00000357376.7	TSL:1	c.-63+6827T>G		intron	N/A	ENSP00000349944.3	Q9NQC3-6
	RTN4	ENST00000394611.6	TSL:1	c.-63+8176T>G		intron	N/A	ENSP00000378109.2	Q9NQC3-6

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101416 AN: 151812 Hom.: 33964 Cov.: 32

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.668 AC: 101475 AN: 151930 Hom.: 33982 Cov.: 32 AF XY: 0.663 AC XY: 49207 AN XY: 74250

African (AFR) AF: 0.666 AC: 27622 AN: 41470

American (AMR) AF: 0.633 AC: 9669 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2093 AN: 3466

East Asian (EAS) AF: 0.666 AC: 3442 AN: 5170

South Asian (SAS) AF: 0.501 AC: 2418 AN: 4826

European-Finnish (FIN) AF: 0.674 AC: 7106 AN: 10546

Middle Eastern (MID) AF: 0.762 AC: 221 AN: 290

European-Non Finnish (NFE) AF: 0.691 AC: 46904 AN: 67868

Other (OTH) AF: 0.685 AC: 1445 AN: 2110

Alfa AF: 0.675 Hom.: 12064

Bravo AF: 0.667

Asia WGS AF: 0.579 AC: 2013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.9
DANN	Benign	0.79
PhyloP100		-0.31
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: rs2972090; hg19: chr2-55269388;