chr4-158410884-A-T

Position:

• chr4-158410884-A-T

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.158410884A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RXFP1	ENST00000460056.6	c.-387-11386A>T		intron_variant		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

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.0131

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.215

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11931209; hg19: chr4-159332036;