rs10518388

Positions:

• chr4-121359180-C-A
• chr4-121359180-C-T

Variant summary

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

The NM_198179.3(QRFPR):​c.341-18570G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0752 in 152,186 control chromosomes in the GnomAD database, including 529 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 0.075 (529 hom., cov: 31)
• Consequence: QRFPR NM_198179.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
QRFPR	NM_198179.3	c.341-18570G>T		intron_variant		ENST00000394427.3	NP_937822.2
QRFPR	XM_017008693.3	c.341-18570G>T		intron_variant			XP_016864182.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
QRFPR	ENST00000394427.3	c.341-18570G>T		intron_variant		1	NM_198179.3	ENSP00000377948	P1
QRFPR	ENST00000512235.1	n.753-18570G>T		intron_variant, non_coding_transcript_variant		1
QRFPR	ENST00000334383.9	c.341-18570G>T		intron_variant		2		ENSP00000335610
QRFPR	ENST00000507331.5	c.341-18570G>T		intron_variant, NMD_transcript_variant		2		ENSP00000423369

Frequencies

GnomAD3 genomes AF: 0.0753 AC: 11449 AN: 152068 Hom.: 529 Cov.: 31

Gnomad AFR AF: 0.0188

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0679

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0807

Gnomad SAS AF: 0.0908

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0705

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0752 AC: 11446 AN: 152186 Hom.: 529 Cov.: 31 AF XY: 0.0752 AC XY: 5592 AN XY: 74368

Gnomad4 AFR AF: 0.0188

Gnomad4 AMR AF: 0.0678

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0805

Gnomad4 SAS AF: 0.0907

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0795

Alfa AF: 0.0815 Hom.: 268

Bravo AF: 0.0654

Asia WGS AF: 0.0850 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.41

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: rs10518388; hg19: chr4-122280335;