NM_198179.3:c.341-3681C>T

Variant names:

• chr4-121344291-G-A
• rs10518387
• NM_198179.3:c.341-3681C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
QRFPR	NM_198179.3	c.341-3681C>T		intron_variant	Intron 1 of 5	ENST00000394427.3	NP_937822.2
QRFPR	XM_017008693.3	c.341-3681C>T		intron_variant	Intron 1 of 3		XP_016864182.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
QRFPR	ENST00000394427.3	c.341-3681C>T		intron_variant	Intron 1 of 5	1	NM_198179.3	ENSP00000377948.2
QRFPR	ENST00000512235.1	n.753-3681C>T		intron_variant	Intron 1 of 1	1
QRFPR	ENST00000334383.9	c.341-3681C>T		intron_variant	Intron 1 of 5	2		ENSP00000335610.5
QRFPR	ENST00000507331.5	n.341-3681C>T		intron_variant	Intron 1 of 6	2		ENSP00000423369.1

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

African (AFR) AF: 0.138 AC: 5731 AN: 41454

American (AMR) AF: 0.221 AC: 3375 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 804 AN: 3464

East Asian (EAS) AF: 0.172 AC: 889 AN: 5178

South Asian (SAS) AF: 0.193 AC: 928 AN: 4816

European-Finnish (FIN) AF: 0.338 AC: 3566 AN: 10544

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.337 AC: 22890 AN: 67950

Other (OTH) AF: 0.256 AC: 540 AN: 2108

Alfa AF: 0.303 Hom.: 4281

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
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10518387; hg19: chr4-122265446;