Genetic Variant QRFPR:c.340+9941A>G (chr4-121370367-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_198179.3(QRFPR):c.340+9941A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.753 in 737,130 control chromosomes in the GnomAD database, including 214,556 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 0.77 ( 45601 hom., cov: 32)

Exomes 𝑓: 0.75 ( 168955 hom. )

Consequence

QRFPR
NM_198179.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.277

Variant links:

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]

QRFPR links:

ENSG00000213480 (HGNC:56785): (KIAA1191 pseudogene 1)

ENSG00000213480 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
QRFPR	NM_198179.3 link	c.340+9941A>G		intron_variant	Intron 1 of 5	ENST00000394427.3	NP_937822.2	Q96P65
QRFPR	XM_017008693.3 link	c.340+9941A>G		intron_variant	Intron 1 of 3		XP_016864182.1	F2Z3L3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
QRFPR	ENST00000394427.3 link	c.340+9941A>G		intron_variant	Intron 1 of 5	1	NM_198179.3	ENSP00000377948.2		Q96P65

Frequencies

GnomAD3 genomes

AF:

0.767

AC:

116695

AN:

152056

Hom.:

45562

Cov.:

show subpopulations

Gnomad AFR

AF:

0.782

Gnomad AMI

AF:

0.877

Gnomad AMR

AF:

0.663

Gnomad ASJ

AF:

0.913

Gnomad EAS

AF:

0.370

Gnomad SAS

AF:

0.628

Gnomad FIN

AF:

0.841

Gnomad MID

AF:

0.801

Gnomad NFE

AF:

0.801

Gnomad OTH

AF:

0.770

GnomAD4 exome

AF:

0.749

AC:

438414

AN:

584956

Hom.:

168955

Cov.:

AF XY:

0.749

AC XY:

239835

AN XY:

320182

show subpopulations

Gnomad4 AFR exome

AF:

0.786

Gnomad4 AMR exome

AF:

0.588

Gnomad4 ASJ exome

AF:

0.905

Gnomad4 EAS exome

AF:

0.367

Gnomad4 SAS exome

AF:

0.660

Gnomad4 FIN exome

AF:

0.837

Gnomad4 NFE exome

AF:

0.802

Gnomad4 OTH exome

AF:

0.767

GnomAD4 genome

AF:

0.767

AC:

116784

AN:

152174

Hom.:

45601

Cov.:

AF XY:

0.763

AC XY:

56741

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.782

Gnomad4 AMR

AF:

0.662

Gnomad4 ASJ

AF:

0.913

Gnomad4 EAS

AF:

0.369

Gnomad4 SAS

AF:

0.630

Gnomad4 FIN

AF:

0.841

Gnomad4 NFE

AF:

0.801

Gnomad4 OTH

AF:

0.767

Alfa

AF:

0.788

Hom.:

24468

Bravo

AF:

0.756

Asia WGS

AF:

0.504

AC:

1755

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

2.3

DANN

Benign

0.65

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over