chr13-31758543-T-C

Position:

• chr13-31758543-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_130806.5(RXFP2):​c.241+139T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 958,014 control chromosomes in the GnomAD database, including 68,725 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.32 (8849 hom., cov: 32)
  • Exomes 𝑓: 0.38 (59876 hom.)
• Consequence: RXFP2 NM_130806.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.511

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 13-31758543-T-C is Benign according to our data. Variant chr13-31758543-T-C is described in ClinVar as [Benign]. Clinvar id is 1277268.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RXFP2	NM_130806.5	c.241+139T>C		intron_variant		ENST00000298386.7	NP_570718.1
RXFP2	NM_001166058.2	c.241+139T>C		intron_variant			NP_001159530.1
RXFP2	XM_017020389.2	c.241+139T>C		intron_variant			XP_016875878.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RXFP2	ENST00000298386.7	c.241+139T>C		intron_variant		1	NM_130806.5	ENSP00000298386.2
RXFP2	ENST00000380314.2	c.241+139T>C		intron_variant		1		ENSP00000369670.1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48864 AN: 152018 Hom.: 8847 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.333

GnomAD4 exome AF: 0.376 AC: 303093 AN: 805878 Hom.: 59876 AF XY: 0.374 AC XY: 153987 AN XY: 411806

Gnomad4 AFR exome AF: 0.142

Gnomad4 AMR exome AF: 0.487

Gnomad4 ASJ exome AF: 0.341

Gnomad4 EAS exome AF: 0.186

Gnomad4 SAS exome AF: 0.330

Gnomad4 FIN exome AF: 0.421

Gnomad4 NFE exome AF: 0.395

Gnomad4 OTH exome AF: 0.360

GnomAD4 genome AF: 0.321 AC: 48871 AN: 152136 Hom.: 8849 Cov.: 32 AF XY: 0.324 AC XY: 24126 AN XY: 74362

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.330

Alfa AF: 0.367 Hom.: 10898

Bravo AF: 0.314

Asia WGS AF: 0.255 AC: 887 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.071
DANN	Benign	0.72

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: rs1571312; hg19: chr13-32332680; COSMIC: COSV53637403;