rs6536309

chr4-158392939-A-Gchr4-158392939-A-T

Variant summary

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

The XR_939403.2(LOC105377510):n.59-126T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,138 control chromosomes in the GnomAD database, including 45,996 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 (45996 hom., cov: 31)
• Consequence: LOC105377510 XR_939403.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

Genes affected

LOC105377510 (HGNC:):

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377510	XR_939403.2	n.59-126T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RXFP1	ENST00000460056.6	c.-387-29331A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117455 AN: 152020 Hom.: 45924 Cov.: 31

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.773 AC: 117590 AN: 152138 Hom.: 45996 Cov.: 31 AF XY: 0.772 AC XY: 57419 AN XY: 74368

Gnomad4 AFR AF: 0.894

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.786

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.748

Alfa AF: 0.720 Hom.: 52119

Bravo AF: 0.785

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.093
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6536309; hg19: chr4-159314091;