4-121329584-AT-A

Position:

• chr4-121329584-AT-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_198179.3(QRFPR):​c.1025del​(p.Asn342MetfsTer10) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000409 in 1,610,262 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as not provided (no stars).

• Frequency:
  • Genomes: 𝑓 0.0020 (1 hom., cov: 33)
  • Exomes 𝑓: 0.00024 (1 hom.)
• Consequence: QRFPR NM_198179.3 frameshift
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 3.12

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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
QRFPR	NM_198179.3	c.1025del	p.Asn342MetfsTer10	frameshift_variant	6/6	ENST00000394427.3	NP_937822.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
QRFPR	ENST00000394427.3	c.1025del	p.Asn342MetfsTer10	frameshift_variant	6/6	1	NM_198179.3	ENSP00000377948	P1
QRFPR	ENST00000334383.9	c.*135del		3_prime_UTR_variant	6/6	2		ENSP00000335610
QRFPR	ENST00000507331.5	c.*583del		3_prime_UTR_variant, NMD_transcript_variant	7/7	2		ENSP00000423369

Frequencies

GnomAD3 genomes AF: 0.00204 AC: 310 AN: 152022 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.00701

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000852

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000416

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.000480

GnomAD3 exomes AF: 0.000634 AC: 157 AN: 247828 Hom.: 0 AF XY: 0.000537 AC XY: 72 AN XY: 133982

Gnomad AFR exome AF: 0.00783

Gnomad AMR exome AF: 0.000622

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000672

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000622

Gnomad OTH exome AF: 0.000166

GnomAD4 exome AF: 0.000239 AC: 349 AN: 1458122 Hom.: 1 Cov.: 31 AF XY: 0.000236 AC XY: 171 AN XY: 725282

Gnomad4 AFR exome AF: 0.00703

Gnomad4 AMR exome AF: 0.000540

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000583

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000442

Gnomad4 OTH exome AF: 0.000531

GnomAD4 genome AF: 0.00203 AC: 309 AN: 152140 Hom.: 1 Cov.: 33 AF XY: 0.00198 AC XY: 147 AN XY: 74382

Gnomad4 AFR AF: 0.00696

Gnomad4 AMR AF: 0.000850

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000416

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.000475

Bravo AF: 0.00227

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

not provided, no classification provided

phenotyping only

GenomeConnect, ClinGen

-

GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.12		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: rs545337361; hg19: chr4-122250739;