rs2972090

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.311
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RTN4NM_020532.5 linkuse as main transcriptc.556+7493T>G intron_variant ENST00000337526.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RTN4ENST00000337526.11 linkuse as main transcriptc.556+7493T>G intron_variant 1 NM_020532.5 Q9NQC3-1

Frequencies

GnomAD3 genomes
AF:
0.668
AC:
101416
AN:
151812
Hom.:
33964
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.666
Gnomad4 AMR
AF:
0.633
Gnomad4 ASJ
AF:
0.604
Gnomad4 EAS
AF:
0.666
Gnomad4 SAS
AF:
0.501
Gnomad4 FIN
AF:
0.674
Gnomad4 NFE
AF:
0.691
Gnomad4 OTH
AF:
0.685
Alfa
AF:
0.674
Hom.:
7052
Bravo
AF:
0.667
Asia WGS
AF:
0.579
AC:
2013
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
8.9
DANN
Benign
0.79

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2972090; hg19: chr2-55269388; API