rs1599793

Variant names:

• chr7-113087129-A-G
• rs1599793
• ENST00000297146.7:c.-289+311T>C

Variant summary

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

The ENST00000297146.7(GPR85):​c.-289+311T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,246 control chromosomes in the GnomAD database, including 1,955 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 0.15 (1955 hom., cov: 32)
• Consequence: GPR85 ENST00000297146.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51
• Publications: 2 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=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR85	NM_001146265.2	c.-289+311T>C		intron_variant	Intron 1 of 2		NP_001139737.1
GPR85	NM_018970.7	c.-286+311T>C		intron_variant	Intron 1 of 2		NP_061843.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR85	ENST00000297146.7	c.-289+311T>C		intron_variant	Intron 1 of 2	1		ENSP00000297146.2
GPR85	ENST00000487573.1	n.339+311T>C		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22916 AN: 152128 Hom.: 1950 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0934

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0533

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.150

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.151 AC: 22926 AN: 152246 Hom.: 1955 Cov.: 32 AF XY: 0.150 AC XY: 11186 AN XY: 74432

African (AFR) AF: 0.119 AC: 4944 AN: 41544

American (AMR) AF: 0.0934 AC: 1429 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3472

East Asian (EAS) AF: 0.0536 AC: 278 AN: 5184

South Asian (SAS) AF: 0.318 AC: 1532 AN: 4816

European-Finnish (FIN) AF: 0.130 AC: 1379 AN: 10612

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12290 AN: 68000

Other (OTH) AF: 0.148 AC: 313 AN: 2110

Alfa AF: 0.166 Hom.: 283

Bravo AF: 0.142

Asia WGS AF: 0.168 AC: 586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.8
DANN	Benign	0.62
PhyloP100		1.5
PromoterAI		0.011	Neutral
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: rs1599793; hg19: chr7-112727184;