dbSNP rs2293369: GPR85:c.*2840G>T (chr7-113080769-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000297146.7(GPR85):c.*2840G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,806 control chromosomes in the GnomAD database, including 16,975 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 0.46 ( 16974 hom., cov: 31)

Exomes 𝑓: 0.50 ( 1 hom. )

Consequence

GPR85
ENST00000297146.7 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0310

Publications

8 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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new If you want to explore the variant's impact on the transcript ENST00000297146.7, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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 (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000297146.7. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GPR85	ENST00000297146.7	TSL:1	c.*2840G>T	3_prime_UTR	Exon 3 of 3	ENSP00000297146.2	P60893
GPR85	ENST00000962376.1		c.*2840G>T	3_prime_UTR	Exon 3 of 3	ENSP00000632435.1
GPR85	ENST00000610164.1	TSL:5	n.*542-255G>T	intron	N/A	ENSP00000476863.1	P60893

Frequencies

GnomAD3 genomes

AF:

0.460

AC:

69840

AN:

151684

Hom.:

16957

Cov.:

show subpopulations

Gnomad AFR

AF:

0.385

Gnomad AMI

AF:

0.373

Gnomad AMR

AF:

0.549

Gnomad ASJ

AF:

0.438

Gnomad EAS

AF:

0.916

Gnomad SAS

AF:

0.340

Gnomad FIN

AF:

0.529

Gnomad MID

AF:

0.279

Gnomad NFE

AF:

0.454

Gnomad OTH

AF:

0.436

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.460

AC:

69897

AN:

151802

Hom.:

16974

Cov.:

AF XY:

0.466

AC XY:

34530

AN XY:

74156

show subpopulations

African (AFR)

AF:

0.385

AC:

15939

AN:

41394

American (AMR)

AF:

0.550

AC:

8393

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.438

AC:

1519

AN:

3470

East Asian (EAS)

AF:

0.917

AC:

4720

AN:

5148

South Asian (SAS)

AF:

0.340

AC:

1634

AN:

4804

European-Finnish (FIN)

AF:

0.529

AC:

5556

AN:

10512

Middle Eastern (MID)

AF:

0.279

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.454

AC:

30803

AN:

67918

Other (OTH)

AF:

0.434

AC:

913

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1830

3661

5491

7322

9152

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

640

1280

1920

2560

3200

<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:

0.443

Hom.:

19051

Bravo

AF:

0.466

Asia WGS

AF:

0.585

AC:

2032

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

1.4

(source)

DANN

Benign

0.46

PhyloP100

0.031

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over