7-113084740-G-T

Variant names:

• chr7-113084740-G-T
• rs1575012
• NM_001146267.2:c.-19C>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001146267.2(GPR85):​c.-19C>A variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.244 in 1,582,912 control chromosomes in the GnomAD database, including 49,344 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 0.24 (4661 hom., cov: 30)
  • Exomes 𝑓: 0.24 (44683 hom.)
• Consequence: GPR85 NM_001146267.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.57
• Publications: 10 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.261 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.-19C>A		5_prime_UTR	Exon 3 of 3	NP_001139739.1
	GPR85	NM_001146265.2		c.-19C>A		5_prime_UTR	Exon 3 of 3	NP_001139737.1
	GPR85	NM_001146266.2		c.-19C>A		5_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.-19C>A		5_prime_UTR	Exon 3 of 3	ENSP00000396763.1
	GPR85	ENST00000297146.7	TSL:1	c.-19C>A		5_prime_UTR	Exon 3 of 3	ENSP00000297146.2
	GPR85	ENST00000449591.2	TSL:1	c.-19C>A		5_prime_UTR	Exon 2 of 2	ENSP00000401178.1

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36506 AN: 151796 Hom.: 4660 Cov.: 30

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.0422

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.272

GnomAD2 exomes AF: 0.234 AC: 54707 AN: 233814 AF XY: 0.240

Gnomad AFR exome AF: 0.225

Gnomad AMR exome AF: 0.180

Gnomad ASJ exome AF: 0.297

Gnomad EAS exome AF: 0.0450

Gnomad FIN exome AF: 0.217

Gnomad NFE exome AF: 0.273

Gnomad OTH exome AF: 0.251

GnomAD4 exome AF: 0.244 AC: 349317 AN: 1431000 Hom.: 44683 Cov.: 30 AF XY: 0.246 AC XY: 174691 AN XY: 711154

African (AFR) AF: 0.231 AC: 7584 AN: 32820

American (AMR) AF: 0.187 AC: 8103 AN: 43220

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 7109 AN: 24704

East Asian (EAS) AF: 0.0354 AC: 1400 AN: 39564

South Asian (SAS) AF: 0.267 AC: 22061 AN: 82738

European-Finnish (FIN) AF: 0.219 AC: 11547 AN: 52608

Middle Eastern (MID) AF: 0.361 AC: 2041 AN: 5646

European-Non Finnish (NFE) AF: 0.252 AC: 274857 AN: 1090426

Other (OTH) AF: 0.247 AC: 14615 AN: 59274

GnomAD4 genome AF: 0.240 AC: 36525 AN: 151912 Hom.: 4661 Cov.: 30 AF XY: 0.236 AC XY: 17500 AN XY: 74260

African (AFR) AF: 0.227 AC: 9402 AN: 41398

American (AMR) AF: 0.227 AC: 3467 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1037 AN: 3470

East Asian (EAS) AF: 0.0419 AC: 216 AN: 5150

South Asian (SAS) AF: 0.260 AC: 1250 AN: 4814

European-Finnish (FIN) AF: 0.220 AC: 2317 AN: 10550

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17948 AN: 67946

Other (OTH) AF: 0.277 AC: 582 AN: 2102

Alfa AF: 0.252 Hom.: 4575

Bravo AF: 0.238

Asia WGS AF: 0.203 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	16
DANN	Benign	0.91
PhyloP100		4.6
Mutation Taster		=300/0	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: rs1575012; hg19: chr7-112724795; COSMIC: COSV51783353;