rs701427

chr22-20245745-A-Cchr22-20245745-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_023004.6(RTN4R):c.23-2635T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 152,060 control chromosomes in the GnomAD database, including 29,271 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 0.62 (29271 hom., cov: 33)
• Consequence: RTN4R NM_023004.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.692

Genes affected

RTN4R (HGNC:18601): (reticulon 4 receptor) This gene encodes the receptor for reticulon 4, oligodendrocyte myelin glycoprotein and myelin-associated glycoprotein. This receptor mediates axonal growth inhibition and may play a role in regulating axonal regeneration and plasticity in the adult central nervous system. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RTN4R	NM_023004.6	c.23-2635T>G		intron_variant		ENST00000043402.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RTN4R	ENST00000043402.8	c.23-2635T>G		intron_variant		1	NM_023004.6	P1

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93854 AN: 151940 Hom.: 29246 Cov.: 33

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.618 AC: 93931 AN: 152060 Hom.: 29271 Cov.: 33 AF XY: 0.614 AC XY: 45681 AN XY: 74366

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.593

Alfa AF: 0.619 Hom.: 29090

Bravo AF: 0.605

Asia WGS AF: 0.596 AC: 2070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.4
Dann	Benign	0.74

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

Other links and lift over

dbSNP: rs701427; hg19: chr22-20233268;