rs6536309

Variant names:

• chr4-158392939-A-G
• rs6536309
• ENST00000460056.6:c.-387-29331A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-158392939-A-G
• chr4-158392939-A-T

Variant summary

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

The ENST00000460056.6(RXFP1):​c.-387-29331A>G variant causes a intron 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: RXFP1 ENST00000460056.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• 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]

ENSG00000250604 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000460056.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RXFP1	ENST00000460056.6	TSL:2	c.-387-29331A>G		intron	N/A	ENSP00000423306.1	E9PCA3
	ENSG00000250604	ENST00000803056.1		n.63-126T>C		intron	N/A
	ENSG00000250604	ENST00000803058.1		n.66-126T>C		intron	N/A

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

African (AFR) AF: 0.894 AC: 37114 AN: 41526

American (AMR) AF: 0.766 AC: 11699 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2028 AN: 3470

East Asian (EAS) AF: 0.896 AC: 4642 AN: 5180

South Asian (SAS) AF: 0.786 AC: 3788 AN: 4820

European-Finnish (FIN) AF: 0.687 AC: 7269 AN: 10576

Middle Eastern (MID) AF: 0.709 AC: 207 AN: 292

European-Non Finnish (NFE) AF: 0.713 AC: 48469 AN: 67982

Other (OTH) AF: 0.748 AC: 1577 AN: 2108

Alfa AF: 0.726 Hom.: 67334

Bravo AF: 0.785

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.093
DANN	Benign	0.37
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6536309;

hg19: chr4-159314091;