rs10518387

chr4-121344291-G-A

Variant summary

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

The NM_198179.3(QRFPR):c.341-3681C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 151,972 control chromosomes in the GnomAD database, including 5,728 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 0.26 (5728 hom., cov: 32)
• Consequence: QRFPR NM_198179.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.74

Genes affected

QRFPR (HGNC:15565): (pyroglutamylated RFamide peptide receptor) Enables G protein-coupled receptor activity. Involved in G protein-coupled receptor signaling pathway. Predicted to be located in non-motile cilium. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
QRFPR	NM_198179.3	c.341-3681C>T		intron_variant		ENST00000394427.3
QRFPR	XM_017008693.3	c.341-3681C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
QRFPR	ENST00000394427.3	c.341-3681C>T		intron_variant		1	NM_198179.3	P1
QRFPR	ENST00000512235.1	n.753-3681C>T		intron_variant, non_coding_transcript_variant		1
QRFPR	ENST00000334383.9	c.341-3681C>T		intron_variant		2
QRFPR	ENST00000507331.5	c.341-3681C>T		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39223 AN: 151854 Hom.: 5728 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.258 AC: 39221 AN: 151972 Hom.: 5728 Cov.: 32 AF XY: 0.256 AC XY: 19023 AN XY: 74258

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.256

Alfa AF: 0.303 Hom.: 3857

Bravo AF: 0.243

Asia WGS AF: 0.194 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.0050
Dann	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518387; hg19: chr4-122265446;