chr4-158427168-T-C

Variant names:

• chr4-158427168-T-C
• rs11100172
• ENST00000460056.6:c.-289+4800T>C

Variant summary

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

The ENST00000460056.6(RXFP1):​c.-289+4800T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,050 control chromosomes in the GnomAD database, including 4,219 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 0.21 (4219 hom., cov: 33)
• Consequence: RXFP1 ENST00000460056.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 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.-289+4800T>C		intron	N/A	ENSP00000423306.1	E9PCA3

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32430 AN: 151930 Hom.: 4205 Cov.: 33

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.214 AC: 32477 AN: 152050 Hom.: 4219 Cov.: 33 AF XY: 0.211 AC XY: 15701 AN XY: 74348

African (AFR) AF: 0.342 AC: 14201 AN: 41490

American (AMR) AF: 0.238 AC: 3627 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 629 AN: 3470

East Asian (EAS) AF: 0.0131 AC: 68 AN: 5184

South Asian (SAS) AF: 0.198 AC: 956 AN: 4828

European-Finnish (FIN) AF: 0.143 AC: 1511 AN: 10586

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

European-Non Finnish (NFE) AF: 0.160 AC: 10870 AN: 67954

Other (OTH) AF: 0.211 AC: 446 AN: 2116

Alfa AF: 0.180 Hom.: 518

Bravo AF: 0.225

Asia WGS AF: 0.153 AC: 531 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.57
PhyloP100		0.47
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: rs11100172; hg19: chr4-159348320;