Variant chr13-31761743-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_130806.5(RXFP2):c.261G>A(p.Ala87Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0548 in 1,610,516 control chromosomes in the GnomAD database, including 2,636 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.048 ( 218 hom., cov: 33)

Exomes 𝑓: 0.055 ( 2418 hom. )

Consequence

RXFP2
NM_130806.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0770

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 13-31761743-G-A is Benign according to our data. Variant chr13-31761743-G-A is described in ClinVar as [Benign]. Clinvar id is 1233360.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.077 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
RXFP2	NM_130806.5 linkuse as main transcript	c.261G>A	p.Ala87Ala	synonymous_variant	3/18	ENST00000298386.7	NP_570718.1
RXFP2	NM_001166058.2 linkuse as main transcript	c.261G>A	p.Ala87Ala	synonymous_variant	3/17		NP_001159530.1
RXFP2	XM_017020389.2 linkuse as main transcript	c.261G>A	p.Ala87Ala	synonymous_variant	3/15		XP_016875878.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RXFP2	ENST00000298386.7 linkuse as main transcript	c.261G>A	p.Ala87Ala	synonymous_variant	3/18	1	NM_130806.5	ENSP00000298386.2		Q8WXD0-1
RXFP2	ENST00000380314.2 linkuse as main transcript	c.261G>A	p.Ala87Ala	synonymous_variant	3/17	1		ENSP00000369670.1		Q8WXD0-2

Frequencies

GnomAD3 genomes

AF:

0.0483

AC:

7352

AN:

152114

Hom.:

217

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0218

Gnomad AMI

AF:

0.0352

Gnomad AMR

AF:

0.0594

Gnomad ASJ

AF:

0.0841

Gnomad EAS

AF:

0.0773

Gnomad SAS

AF:

0.0305

Gnomad FIN

AF:

0.0438

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0597

Gnomad OTH

AF:

0.0549

GnomAD3 exomes

AF:

0.0511

AC:

12847

AN:

251202

Hom.:

419

AF XY:

0.0516

AC XY:

7005

AN XY:

135750

show subpopulations

Gnomad AFR exome

AF:

0.0204

Gnomad AMR exome

AF:

0.0388

Gnomad ASJ exome

AF:

0.0790

Gnomad EAS exome

AF:

0.0697

Gnomad SAS exome

AF:

0.0310

Gnomad FIN exome

AF:

0.0486

Gnomad NFE exome

AF:

0.0595

Gnomad OTH exome

AF:

0.0558

GnomAD4 exome

AF:

0.0555

AC:

80921

AN:

1458284

Hom.:

2418

Cov.:

AF XY:

0.0548

AC XY:

39798

AN XY:

725656

show subpopulations

Gnomad4 AFR exome

AF:

0.0227

Gnomad4 AMR exome

AF:

0.0393

Gnomad4 ASJ exome

AF:

0.0788

Gnomad4 EAS exome

AF:

0.0773

Gnomad4 SAS exome

AF:

0.0320

Gnomad4 FIN exome

AF:

0.0489

Gnomad4 NFE exome

AF:

0.0577

Gnomad4 OTH exome

AF:

0.0582

GnomAD4 genome

AF:

0.0483

AC:

7351

AN:

152232

Hom.:

218

Cov.:

AF XY:

0.0482

AC XY:

3589

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.0218

Gnomad4 AMR

AF:

0.0595

Gnomad4 ASJ

AF:

0.0841

Gnomad4 EAS

AF:

0.0775

Gnomad4 SAS

AF:

0.0305

Gnomad4 FIN

AF:

0.0438

Gnomad4 NFE

AF:

0.0597

Gnomad4 OTH

AF:

0.0553

Alfa

AF:

0.0547

Hom.:

317

Bravo

AF:

0.0475

Asia WGS

AF:

0.0450

AC:

156

AN:

3476

EpiCase

AF:

0.0642

EpiControl

AF:

0.0639

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 09, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

5.6

DANN

Benign

0.60

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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