Variant chr13-31758419-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_130806.5(RXFP2):c.241+15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 1,613,246 control chromosomes in the GnomAD database, including 25,566 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.18 ( 2478 hom., cov: 32)

Exomes 𝑓: 0.18 ( 23088 hom. )

Consequence

RXFP2
NM_130806.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.377

Variant links:

Genes affected

RXFP2 (HGNC:17318): (relaxin family peptide receptor 2) This gene encodes a member of the GPCR (G protein-coupled, 7-transmembrane receptor) family. Mutations in this gene are associated with cryptorchidism. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2009]

RXFP2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 13-31758419-C-T is Benign according to our data. Variant chr13-31758419-C-T is described in ClinVar as [Benign]. Clinvar id is 1229034.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
RXFP2	NM_130806.5 linkuse as main transcript	c.241+15C>T	intron_variant	ENST00000298386.7
RXFP2	NM_001166058.2 linkuse as main transcript	c.241+15C>T	intron_variant
RXFP2	XM_017020389.2 linkuse as main transcript	c.241+15C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RXFP2	ENST00000298386.7 linkuse as main transcript	c.241+15C>T		intron_variant		1	NM_130806.5	P1	Q8WXD0-1
RXFP2	ENST00000380314.2 linkuse as main transcript	c.241+15C>T		intron_variant		1			Q8WXD0-2

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27725

AN:

151912

Hom.:

2478

Cov.:

show subpopulations

Gnomad AFR

AF:

0.179

Gnomad AMI

AF:

0.284

Gnomad AMR

AF:

0.171

Gnomad ASJ

AF:

0.219

Gnomad EAS

AF:

0.227

Gnomad SAS

AF:

0.237

Gnomad FIN

AF:

0.204

Gnomad MID

AF:

0.229

Gnomad NFE

AF:

0.173

Gnomad OTH

AF:

0.192

GnomAD3 exomes

AF:

0.189

AC:

47577

AN:

251180

Hom.:

4542

AF XY:

0.192

AC XY:

26104

AN XY:

135768

show subpopulations

Gnomad AFR exome

AF:

0.172

Gnomad AMR exome

AF:

0.182

Gnomad ASJ exome

AF:

0.210

Gnomad EAS exome

AF:

0.242

Gnomad SAS exome

AF:

0.219

Gnomad FIN exome

AF:

0.194

Gnomad NFE exome

AF:

0.174

Gnomad OTH exome

AF:

0.200

GnomAD4 exome

AF:

0.175

AC:

256090

AN:

1461212

Hom.:

23088

Cov.:

AF XY:

0.177

AC XY:

128779

AN XY:

726922

show subpopulations

Gnomad4 AFR exome

AF:

0.173

Gnomad4 AMR exome

AF:

0.180

Gnomad4 ASJ exome

AF:

0.215

Gnomad4 EAS exome

AF:

0.235

Gnomad4 SAS exome

AF:

0.219

Gnomad4 FIN exome

AF:

0.200

Gnomad4 NFE exome

AF:

0.167

Gnomad4 OTH exome

AF:

0.181

GnomAD4 genome

AF:

0.182

AC:

27742

AN:

152034

Hom.:

2478

Cov.:

AF XY:

0.184

AC XY:

13657

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.179

Gnomad4 AMR

AF:

0.171

Gnomad4 ASJ

AF:

0.219

Gnomad4 EAS

AF:

0.227

Gnomad4 SAS

AF:

0.237

Gnomad4 FIN

AF:

0.204

Gnomad4 NFE

AF:

0.173

Gnomad4 OTH

AF:

0.192

Alfa

AF:

0.178

Hom.:

475

Bravo

AF:

0.181

Asia WGS

AF:

0.237

AC:

824

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.70

DANN

Benign

0.52

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over