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

Variant summary

Our verdict is Benign. The variant received -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

Publications

4 publications found

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:

KIAA1191P1 (HGNC:56785): (KIAA1191 pseudogene 1)

KIAA1191P1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198179.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	QRFPR	NM_198179.3	MANE Select	c.340+9941A>G		intron	N/A	NP_937822.2	Q96P65

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
QRFPR	ENST00000394427.3	TSL:1 MANE Select	c.340+9941A>G	intron	N/A	ENSP00000377948.2	Q96P65
QRFPR	ENST00000512235.1	TSL:1	n.752+9941A>G	intron	N/A
QRFPR	ENST00000970622.1		c.340+9941A>G	intron	N/A	ENSP00000640681.1

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

African (AFR)

AF:

0.786

AC:

12957

AN:

16476

American (AMR)

AF:

0.588

AC:

24552

AN:

41752

Ashkenazi Jewish (ASJ)

AF:

0.905

AC:

17662

AN:

19508

East Asian (EAS)

AF:

0.367

AC:

12214

AN:

33276

South Asian (SAS)

AF:

0.660

AC:

45541

AN:

68992

European-Finnish (FIN)

AF:

0.837

AC:

40026

AN:

47840

Middle Eastern (MID)

AF:

0.863

AC:

1951

AN:

2260

European-Non Finnish (NFE)

AF:

0.802

AC:

260579

AN:

324968

Other (OTH)

AF:

0.767

AC:

22932

AN:

29884

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.551

Heterozygous variant carriers

4377

8754

13130

17507

21884

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1160

2320

3480

4640

5800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.767

AC:

116784

AN:

152174

Hom.:

45601

Cov.:

AF XY:

0.763

AC XY:

56741

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.782

AC:

32478

AN:

41506

American (AMR)

AF:

0.662

AC:

10125

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.913

AC:

3169

AN:

3472

East Asian (EAS)

AF:

0.369

AC:

1905

AN:

5160

South Asian (SAS)

AF:

0.630

AC:

3038

AN:

4824

European-Finnish (FIN)

AF:

0.841

AC:

8913

AN:

10598

Middle Eastern (MID)

AF:

0.803

AC:

236

AN:

294

European-Non Finnish (NFE)

AF:

0.801

AC:

54499

AN:

68004

Other (OTH)

AF:

0.767

AC:

1621

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1346

2692

4037

5383

6729

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

850

1700

2550

3400

4250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.789

Hom.:

27216

Bravo

AF:

0.756

Asia WGS

AF:

0.504

AC:

1755

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

2.3

(source)

DANN

Benign

0.65

PhyloP100

-0.28

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over