Genetic Variant RXFP2:c.241+120T>A (chr13-31758524-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_130806.5(RXFP2):c.241+120T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

RXFP2
NM_130806.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.674

Publications

3 publications found

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 Gene-Disease associations (from GenCC):

cryptorchidism
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

RXFP2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
RXFP2	NM_130806.5 link	c.241+120T>A	intron_variant	Intron 2 of 17	ENST00000298386.7	NP_570718.1
RXFP2	NM_001166058.2 link	c.241+120T>A	intron_variant	Intron 2 of 16		NP_001159530.1
RXFP2	XM_017020389.2 link	c.241+120T>A	intron_variant	Intron 2 of 14		XP_016875878.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RXFP2	ENST00000298386.7 link	c.241+120T>A		intron_variant	Intron 2 of 17	1	NM_130806.5	ENSP00000298386.2		Q8WXD0-1
RXFP2	ENST00000380314.2 link	c.241+120T>A		intron_variant	Intron 2 of 16	1		ENSP00000369670.1		Q8WXD0-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1010906

Hom.:

AF XY:

0.00

AC XY:

AN XY:

511334

African (AFR)

AF:

0.00

AC:

AN:

24326

American (AMR)

AF:

0.00

AC:

AN:

36008

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19948

East Asian (EAS)

AF:

0.00

AC:

AN:

36810

South Asian (SAS)

AF:

0.00

AC:

AN:

67024

European-Finnish (FIN)

AF:

0.00

AC:

AN:

47560

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3062

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

731236

Other (OTH)

AF:

0.00

AC:

AN:

44932

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.3

(source)

DANN

Benign

0.46

PhyloP100

0.67

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over