rs1599792

Positions:

• chr7-113087268-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000297146.7(GPR85):​c.-289+172C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,064 control chromosomes in the GnomAD database, including 2,181 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 0.16 (2181 hom., cov: 32)
• Consequence: GPR85 ENST00000297146.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPR85	NM_001146265.2	c.-289+172C>T		intron_variant			NP_001139737.1
GPR85	NM_018970.7	c.-286+172C>T		intron_variant			NP_061843.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPR85	ENST00000297146.7	c.-289+172C>T		intron_variant		1		ENSP00000297146	P1
GPR85	ENST00000487573.1	n.339+172C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24620 AN: 151946 Hom.: 2174 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0988

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0530

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.162 AC: 24630 AN: 152064 Hom.: 2181 Cov.: 32 AF XY: 0.162 AC XY: 12020 AN XY: 74330

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.0987

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.0534

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.156

Alfa AF: 0.174 Hom.: 306

Bravo AF: 0.156

Asia WGS AF: 0.168 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	11
DANN	Benign	0.77

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

LitVar

Other links and lift over

dbSNP: rs1599792; hg19: chr7-112727323;