Genetic Variant GPR85:c.*143T>A (chr7-113083466-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001146267.2(GPR85):c.*143T>A variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.06 in 744,784 control chromosomes in the GnomAD database, including 1,529 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 0.058 ( 308 hom., cov: 32)

Exomes 𝑓: 0.060 ( 1221 hom. )

Consequence

GPR85
NM_001146267.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.96

Publications

7 publications found

Variant links:

Genes affected

GPR85 (HGNC:4536): (G protein-coupled receptor 85) Members of the G protein-coupled receptor (GPCR) family, such as GPR85, have a similar structure characterized by 7 transmembrane domains. Activation of GPCRs by extracellular stimuli, such as neurotransmitters, hormones, or light, induces an intracellular signaling cascade mediated by heterotrimeric GTP-binding proteins, or G proteins (Matsumoto et al., 2000 [PubMed 10833454]).[supplied by OMIM, Aug 2008]

GPR85 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=-0.49).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0652 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001146267.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GPR85	NM_001146267.2	MANE Select	c.*143T>A	3_prime_UTR	Exon 3 of 3	NP_001139739.1	P60893
GPR85	NM_001146265.2		c.*143T>A	3_prime_UTR	Exon 3 of 3	NP_001139737.1	A4D0T8
GPR85	NM_001146266.2		c.*143T>A	3_prime_UTR	Exon 2 of 2	NP_001139738.1	A4D0T8

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GPR85	ENST00000424100.2	TSL:1 MANE Select	c.*143T>A	3_prime_UTR	Exon 3 of 3	ENSP00000396763.1	P60893
GPR85	ENST00000297146.7	TSL:1	c.*143T>A	3_prime_UTR	Exon 3 of 3	ENSP00000297146.2	P60893
GPR85	ENST00000449591.2	TSL:1	c.*143T>A	3_prime_UTR	Exon 2 of 2	ENSP00000401178.1	P60893

Frequencies

GnomAD3 genomes

AF:

0.0583

AC:

8864

AN:

152128

Hom.:

309

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0599

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.0687

Gnomad ASJ

AF:

0.0490

Gnomad EAS

AF:

0.00115

Gnomad SAS

AF:

0.0707

Gnomad FIN

AF:

0.0469

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0595

Gnomad OTH

AF:

0.0727

GnomAD4 exome

AF:

0.0605

AC:

35842

AN:

592538

Hom.:

1221

Cov.:

AF XY:

0.0611

AC XY:

19076

AN XY:

312298

show subpopulations

African (AFR)

AF:

0.0650

AC:

1014

AN:

15602

American (AMR)

AF:

0.0798

AC:

2105

AN:

26378

Ashkenazi Jewish (ASJ)

AF:

0.0535

AC:

800

AN:

14954

East Asian (EAS)

AF:

0.000227

AC:

AN:

35304

South Asian (SAS)

AF:

0.0783

AC:

4005

AN:

51136

European-Finnish (FIN)

AF:

0.0485

AC:

2172

AN:

44772

Middle Eastern (MID)

AF:

0.0888

AC:

195

AN:

2196

European-Non Finnish (NFE)

AF:

0.0635

AC:

23565

AN:

371326

Other (OTH)

AF:

0.0641

AC:

1978

AN:

30870

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1603

3207

4810

6414

8017

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

406

812

1218

1624

2030

<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:

0.0582

AC:

8866

AN:

152246

Hom.:

308

Cov.:

AF XY:

0.0583

AC XY:

4338

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.0598

AC:

2487

AN:

41562

American (AMR)

AF:

0.0686

AC:

1048

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0490

AC:

170

AN:

3470

East Asian (EAS)

AF:

0.00116

AC:

AN:

5188

South Asian (SAS)

AF:

0.0711

AC:

343

AN:

4822

European-Finnish (FIN)

AF:

0.0469

AC:

497

AN:

10602

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0594

AC:

4043

AN:

68008

Other (OTH)

AF:

0.0714

AC:

151

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

428

856

1283

1711

2139

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

216

324

432

540

<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:

0.0555

Hom.:

Bravo

AF:

0.0604

Asia WGS

AF:

0.0280

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

(source)

DANN

Benign

0.71

PhyloP100

4.0

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