rs2346793

Positions:

• chr4-158444532-G-T

Variant summary

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

The ENST00000460056.6(RXFP1):​c.-289+22164G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,202 control chromosomes in the GnomAD database, including 3,625 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 0.20 (3625 hom., cov: 33)
• Consequence: RXFP1 ENST00000460056.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RXFP1	ENST00000460056.6	c.-289+22164G>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30698 AN: 152084 Hom.: 3614 Cov.: 33

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.202 AC: 30734 AN: 152202 Hom.: 3625 Cov.: 33 AF XY: 0.200 AC XY: 14907 AN XY: 74414

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.0131

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.200

Alfa AF: 0.176 Hom.: 457

Bravo AF: 0.212

Asia WGS AF: 0.151 AC: 524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.73
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2346793; hg19: chr4-159365684;