rs10032252

Variant names:

• chr4-158456322-G-A
• rs10032252
• ENST00000460056.6:c.-289+33954G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000460056.6(RXFP1):​c.-289+33954G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 151,990 control chromosomes in the GnomAD database, including 46,229 homozygotes. 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: 𝑓 0.77 (46229 hom., cov: 31)
• Consequence: RXFP1 ENST00000460056.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619

Genes affected

RXFP1 (HGNC:19718): (relaxin family peptide receptor 1) This gene encodes a member of the leucine-rich repeat-containing subgroup of the G protein-coupled 7-transmembrane receptor superfamily. The encoded protein plays a critical role in sperm motility, pregnancy and parturition as a receptor for the protein hormone relaxin. Decreased expression of this gene may play a role in endometriosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RXFP1	ENST00000460056.6	c.-289+33954G>A		intron_variant	Intron 2 of 19	2		ENSP00000423306.1

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117049 AN: 151872 Hom.: 46203 Cov.: 31

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.778

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.771 AC: 117116 AN: 151990 Hom.: 46229 Cov.: 31 AF XY: 0.774 AC XY: 57480 AN XY: 74294

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.755

Gnomad4 ASJ AF: 0.818

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.779

Alfa AF: 0.808 Hom.: 8500

Bravo AF: 0.756

Asia WGS AF: 0.844 AC: 2938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10032252; hg19: chr4-159377474;