Genetic Variant GPR132:n.*2274G>A (chr14-105049889-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000551869.1(GPR132):n.*2274G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,320 control chromosomes in the GnomAD database, including 22,284 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 0.51 ( 22264 hom., cov: 34)

Exomes 𝑓: 0.61 ( 20 hom. )

Consequence

GPR132
ENST00000551869.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.556

Publications

2 publications found

Variant links:

Genes affected

GPR132 (HGNC:17482): (G protein-coupled receptor 132) This gene encodes a member of the guanine nucleotide-binding protein (G protein)-coupled receptor (GPCR) superfamily. The receptors are seven-pass transmembrane proteins that respond to extracellular cues and activate intracellular signal transduction pathways. This protein was reported to be a receptor for lysophosphatidylcholine action, but PubMedID: 15653487 retracts this finding and instead suggests this protein to be an effector of lysophosphatidylcholine action. This protein may have proton-sensing activity and may be a receptor for oxidized free fatty acids. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

GPR132 links:

LINC02298 (HGNC:53216): (long intergenic non-protein coding RNA 2298)

LINC02298 links:

LOC124903398 (HGNC:):

LOC124903398 links:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000551869.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
GPR132	NM_013345.4	MANE Select	c.*1105G>A	3_prime_UTR	Exon 4 of 4	NP_037477.1
GPR132	NM_001278694.2		c.*1105G>A	3_prime_UTR	Exon 5 of 5	NP_001265623.1
GPR132	NM_001278695.2		c.*1105G>A	3_prime_UTR	Exon 3 of 3	NP_001265624.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
GPR132	ENST00000551869.1	TSL:1	n.*2274G>A	non_coding_transcript_exon	Exon 3 of 3	ENSP00000448513.1
GPR132	ENST00000329797.8	TSL:1 MANE Select	c.*1105G>A	3_prime_UTR	Exon 4 of 4	ENSP00000328818.3
GPR132	ENST00000392585.2	TSL:1	c.*1105G>A	3_prime_UTR	Exon 3 of 3	ENSP00000376364.2

Frequencies

GnomAD3 genomes

AF:

0.506

AC:

76979

AN:

152088

Hom.:

22267

Cov.:

show subpopulations

Gnomad AFR

AF:

0.225

Gnomad AMI

AF:

0.543

Gnomad AMR

AF:

0.531

Gnomad ASJ

AF:

0.664

Gnomad EAS

AF:

0.297

Gnomad SAS

AF:

0.532

Gnomad FIN

AF:

0.651

Gnomad MID

AF:

0.627

Gnomad NFE

AF:

0.653

Gnomad OTH

AF:

0.543

GnomAD4 exome

AF:

0.614

AC:

AN:

114

Hom.:

Cov.:

AF XY:

0.635

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.638

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.506

AC:

76989

AN:

152206

Hom.:

22264

Cov.:

AF XY:

0.505

AC XY:

37608

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.224

AC:

9327

AN:

41548

American (AMR)

AF:

0.530

AC:

8109

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.664

AC:

2303

AN:

3470

East Asian (EAS)

AF:

0.296

AC:

1533

AN:

5172

South Asian (SAS)

AF:

0.533

AC:

2568

AN:

4820

European-Finnish (FIN)

AF:

0.651

AC:

6893

AN:

10592

Middle Eastern (MID)

AF:

0.627

AC:

183

AN:

292

European-Non Finnish (NFE)

AF:

0.653

AC:

44430

AN:

67994

Other (OTH)

AF:

0.543

AC:

1149

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1753

3506

5260

7013

8766

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

672

1344

2016

2688

3360

<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:

0.537

Hom.:

3089

Bravo

AF:

0.486

Asia WGS

AF:

0.411

AC:

1429

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.1

(source)

DANN

Benign

0.43

PhyloP100

-0.56

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

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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