rs2140913

Variant names:

• chr7-113087998-C-A
• rs2140913
• ENST00000297146.7:c.-847G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-113087998-C-A
• chr7-113087998-C-G

Variant summary

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

The ENST00000297146.7(GPR85):​c.-847G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,166 control chromosomes in the GnomAD database, including 51,811 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 0.82 (51811 hom., cov: 32)
• Consequence: GPR85 ENST00000297146.7 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR85	ENST00000297146.7	c.-847G>T		upstream_gene_variant		1		ENSP00000297146.2
GPR85	ENST00000487573.1	n.-220G>T		upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125236 AN: 152048 Hom.: 51774 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.824 AC: 125324 AN: 152166 Hom.: 51811 Cov.: 32 AF XY: 0.824 AC XY: 61335 AN XY: 74414

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.896

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.820

Gnomad4 OTH AF: 0.835

Alfa AF: 0.823 Hom.: 49911

Bravo AF: 0.828

Asia WGS AF: 0.825 AC: 2865 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.15
DANN	Benign	0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2140913; hg19: chr7-112728053;