rs870266

Variant names:

• chr7-113083466-A-G
• rs870266
• NM_001146267.2:c.*143T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-113083466-A-G
• chr7-113083466-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001146267.2(GPR85):​c.*143T>C variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.00000843 in 592,848 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000084 (0 hom.)
• Consequence: GPR85 NM_001146267.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.96
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR85	NM_001146267.2	c.*143T>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000424100.2	NP_001139739.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR85	ENST00000424100.2	c.*143T>C		3_prime_UTR_variant	Exon 3 of 3	1	NM_001146267.2	ENSP00000396763.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000843 AC: 5 AN: 592848 Hom.: 0 Cov.: 8 AF XY: 0.0000160 AC XY: 5 AN XY: 312454

African (AFR) AF: 0.00 AC: 0 AN: 15608

American (AMR) AF: 0.00 AC: 0 AN: 26410

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14956

East Asian (EAS) AF: 0.00 AC: 0 AN: 35304

South Asian (SAS) AF: 0.0000977 AC: 5 AN: 51186

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44796

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2200

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 371510

Other (OTH) AF: 0.00 AC: 0 AN: 30878

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	17
DANN	Benign	0.79
PhyloP100		4.0

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: rs870266; hg19: chr7-112723521;