rs1581688

Variant names:

• chr7-113083038-T-C
• rs1581688
• NM_001146267.2:c.*571A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.456
• Publications: 6 publications found

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]

ACMG classification

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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR85	NM_001146267.2	MANE Select	c.*571A>G		3_prime_UTR	Exon 3 of 3	NP_001139739.1
	GPR85	NM_001146265.2		c.*571A>G		3_prime_UTR	Exon 3 of 3	NP_001139737.1
	GPR85	NM_001146266.2		c.*571A>G		3_prime_UTR	Exon 2 of 2	NP_001139738.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR85	ENST00000424100.2	TSL:1 MANE Select	c.*571A>G		3_prime_UTR	Exon 3 of 3	ENSP00000396763.1
	GPR85	ENST00000297146.7	TSL:1	c.*571A>G		3_prime_UTR	Exon 3 of 3	ENSP00000297146.2
	GPR85	ENST00000449591.2	TSL:1	c.*571A>G		3_prime_UTR	Exon 2 of 2	ENSP00000401178.1

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49619 AN: 151930 Hom.: 8447 Cov.: 32

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.: 24 Cov.: 0 AF XY: 0.290 AC XY: 91 AN XY: 314

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.250 AC: 1 AN: 4

European-Finnish (FIN) AF: 0.304 AC: 130 AN: 428

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.276 AC: 21 AN: 76

Other (OTH) AF: 0.333 AC: 2 AN: 6

GnomAD4 genome AF: 0.327 AC: 49651 AN: 152048 Hom.: 8454 Cov.: 32 AF XY: 0.321 AC XY: 23884 AN XY: 74312

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	7.8
DANN	Benign	0.70
PhyloP100		0.46
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1581688; hg19: chr7-112723093;