chr13-31761903-C-T

Position:

• chr13-31761903-C-T

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.319+102C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 778,984 control chromosomes in the GnomAD database, including 55,995 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.33 (9004 hom., cov: 33)
  • Exomes 𝑓: 0.38 (46991 hom.)
• Consequence: RXFP2 NM_130806.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.115

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=-0.89).
• BP6: Variant 13-31761903-C-T is Benign according to our data. Variant chr13-31761903-C-T is described in ClinVar as [Benign]. Clinvar id is 1226064.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RXFP2	NM_130806.5	c.319+102C>T		intron_variant		ENST00000298386.7	NP_570718.1
RXFP2	NM_001166058.2	c.319+102C>T		intron_variant			NP_001159530.1
RXFP2	XM_017020389.2	c.319+102C>T		intron_variant			XP_016875878.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RXFP2	ENST00000298386.7	c.319+102C>T		intron_variant		1	NM_130806.5	ENSP00000298386.2
RXFP2	ENST00000380314.2	c.319+102C>T		intron_variant		1		ENSP00000369670.1

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49743 AN: 151886 Hom.: 9001 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.336

GnomAD4 exome AF: 0.379 AC: 237680 AN: 626978 Hom.: 46991 AF XY: 0.376 AC XY: 125835 AN XY: 335076

Gnomad4 AFR exome AF: 0.170

Gnomad4 AMR exome AF: 0.495

Gnomad4 ASJ exome AF: 0.349

Gnomad4 EAS exome AF: 0.187

Gnomad4 SAS exome AF: 0.331

Gnomad4 FIN exome AF: 0.430

Gnomad4 NFE exome AF: 0.398

Gnomad4 OTH exome AF: 0.362

GnomAD4 genome AF: 0.327 AC: 49765 AN: 152006 Hom.: 9004 Cov.: 33 AF XY: 0.330 AC XY: 24541 AN XY: 74278

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.333

Alfa AF: 0.376 Hom.: 20198

Bravo AF: 0.321

Asia WGS AF: 0.257 AC: 895 AN: 3476

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 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1536635; hg19: chr13-32336040; COSMIC: COSV53638491;