rs11931209

Variant names:

• chr4-158410884-A-T
• rs11931209
• ENST00000460056.6:c.-387-11386A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000460056.6(RXFP1):​c.-387-11386A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,114 control chromosomes in the GnomAD database, including 4,708 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 0.22 (4708 hom., cov: 33)
• Consequence: RXFP1 ENST00000460056.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.368 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.-387-11386A>T		intron_variant	Intron 1 of 19	2		ENSP00000423306.1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33792 AN: 151996 Hom.: 4691 Cov.: 33

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.222 AC: 33839 AN: 152114 Hom.: 4708 Cov.: 33 AF XY: 0.220 AC XY: 16334 AN XY: 74382

African (AFR) AF: 0.373 AC: 15466 AN: 41454

American (AMR) AF: 0.242 AC: 3701 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 630 AN: 3472

East Asian (EAS) AF: 0.0131 AC: 68 AN: 5176

South Asian (SAS) AF: 0.197 AC: 952 AN: 4824

European-Finnish (FIN) AF: 0.143 AC: 1511 AN: 10582

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10889 AN: 68008

Other (OTH) AF: 0.215 AC: 453 AN: 2110

Alfa AF: 0.183 Hom.: 398

Bravo AF: 0.236

Asia WGS AF: 0.155 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.27
DANN	Benign	0.55
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11931209; hg19: chr4-159332036;