13-31758155-C-G

Position:

• chr13-31758155-C-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_130806.5(RXFP2):​c.95-103C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0816 in 1,107,404 control chromosomes in the GnomAD database, including 4,014 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.083 (528 hom., cov: 32)
  • Exomes 𝑓: 0.081 (3486 hom.)
• Consequence: RXFP2 NM_130806.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.626

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 13-31758155-C-G is Benign according to our data. Variant chr13-31758155-C-G is described in ClinVar as [Benign]. Clinvar id is 1239108.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RXFP2	NM_130806.5	c.95-103C>G		intron_variant		ENST00000298386.7	NP_570718.1
RXFP2	NM_001166058.2	c.95-103C>G		intron_variant			NP_001159530.1
RXFP2	XM_017020389.2	c.95-103C>G		intron_variant			XP_016875878.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RXFP2	ENST00000298386.7	c.95-103C>G		intron_variant		1	NM_130806.5	ENSP00000298386.2
RXFP2	ENST00000380314.2	c.95-103C>G		intron_variant		1		ENSP00000369670.1

Frequencies

GnomAD3 genomes AF: 0.0827 AC: 12572 AN: 152046 Hom.: 527 Cov.: 32

Gnomad AFR AF: 0.0746

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.0872

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0820

Gnomad SAS AF: 0.0682

Gnomad FIN AF: 0.0669

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0876

Gnomad OTH AF: 0.0938

GnomAD4 exome AF: 0.0814 AC: 77793 AN: 955240 Hom.: 3486 AF XY: 0.0820 AC XY: 40797 AN XY: 497816

Gnomad4 AFR exome AF: 0.0757

Gnomad4 AMR exome AF: 0.0557

Gnomad4 ASJ exome AF: 0.119

Gnomad4 EAS exome AF: 0.0832

Gnomad4 SAS exome AF: 0.0764

Gnomad4 FIN exome AF: 0.0800

Gnomad4 NFE exome AF: 0.0820

Gnomad4 OTH exome AF: 0.0879

GnomAD4 genome AF: 0.0826 AC: 12570 AN: 152164 Hom.: 528 Cov.: 32 AF XY: 0.0821 AC XY: 6105 AN XY: 74392

Gnomad4 AFR AF: 0.0744

Gnomad4 AMR AF: 0.0872

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.0822

Gnomad4 SAS AF: 0.0682

Gnomad4 FIN AF: 0.0669

Gnomad4 NFE AF: 0.0876

Gnomad4 OTH AF: 0.0938

Alfa AF: 0.0895 Hom.: 90

Bravo AF: 0.0814

Asia WGS AF: 0.0690 AC: 241 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 20, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.96
DANN	Benign	0.36

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: rs9548977; hg19: chr13-32332292; COSMIC: COSV53639916;