dbSNP rs1581688: GPR85:c.*571A>G (chr7-113083038-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_001146267.2(GPR85):c.*571A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,566 control chromosomes in the GnomAD database, including 8,478 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 0.33 ( 8454 hom., cov: 32)

Exomes 𝑓: 0.30 ( 24 hom. )

Consequence

GPR85
NM_001146267.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.456

Publications

6 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:

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=-0.52).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR85	NM_001146267.2 link	c.*571A>G		3_prime_UTR_variant	Exon 3 of 3	ENST00000424100.2	NP_001139739.1	P60893A4D0T8Q8NEN2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GPR85	ENST00000424100.2 link	c.*571A>G	3_prime_UTR_variant	Exon 3 of 3	1	NM_001146267.2	ENSP00000396763.1	P60893
GPR85	ENST00000297146.7 link	c.*571A>G	3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000297146.2	P60893
GPR85	ENST00000449591.2 link	c.*571A>G	3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000401178.1	P60893
GPR85	ENST00000610164.1 link	n.*541+30A>G	intron_variant	Intron 2 of 2	5		ENSP00000476863.1	P60893

Frequencies

GnomAD3 genomes

AF:

0.327

AC:

49619

AN:

151930

Hom.:

8447

Cov.:

show subpopulations

Gnomad AFR

AF:

0.294

Gnomad AMI

AF:

0.285

Gnomad AMR

AF:

0.283

Gnomad ASJ

AF:

0.380

Gnomad EAS

AF:

0.0577

Gnomad SAS

AF:

0.394

Gnomad FIN

AF:

0.315

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.371

Gnomad OTH

AF:

0.344

GnomAD4 exome

AF:

0.297

AC:

154

AN:

518

Hom.:

Cov.:

AF XY:

0.290

AC XY:

AN XY:

314

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.304

AC:

130

AN:

428

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.276

AC:

AN:

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.327

AC:

49651

AN:

152048

Hom.:

8454

Cov.:

AF XY:

0.321

AC XY:

23884

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.294

AC:

12196

AN:

41500

American (AMR)

AF:

0.283

AC:

4316

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.380

AC:

1319

AN:

3468

East Asian (EAS)

AF:

0.0574

AC:

297

AN:

5172

South Asian (SAS)

AF:

0.395

AC:

1904

AN:

4818

European-Finnish (FIN)

AF:

0.315

AC:

3327

AN:

10552

Middle Eastern (MID)

AF:

0.395

AC:

116

AN:

294

European-Non Finnish (NFE)

AF:

0.371

AC:

25181

AN:

67952

Other (OTH)

AF:

0.348

AC:

736

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1683

3366

5049

6732

8415

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.354

Hom.:

29398

Bravo

AF:

0.319

Asia WGS

AF:

0.270

AC:

940

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

7.8

(source)

DANN

Benign

0.70

PhyloP100

0.46

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.

rs1581688

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over