chr7-113080769-C-A

Variant names:

• chr7-113080769-C-A
• rs2293369
• ENST00000297146.7:c.*2840G>T

Variant summary

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

The ENST00000297146.7(GPR85):​c.*2840G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,806 control chromosomes in the GnomAD database, including 16,975 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 0.46 (16974 hom., cov: 31)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: GPR85 ENST00000297146.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 8 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 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.*2840G>T		3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000297146.2
GPR85	ENST00000610164.1	n.*542-255G>T		intron_variant	Intron 2 of 2	5		ENSP00000476863.1

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69840 AN: 151684 Hom.: 16957 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.279

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.436

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.460 AC: 69897 AN: 151802 Hom.: 16974 Cov.: 31 AF XY: 0.466 AC XY: 34530 AN XY: 74156

African (AFR) AF: 0.385 AC: 15939 AN: 41394

American (AMR) AF: 0.550 AC: 8393 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1519 AN: 3470

East Asian (EAS) AF: 0.917 AC: 4720 AN: 5148

South Asian (SAS) AF: 0.340 AC: 1634 AN: 4804

European-Finnish (FIN) AF: 0.529 AC: 5556 AN: 10512

Middle Eastern (MID) AF: 0.279 AC: 81 AN: 290

European-Non Finnish (NFE) AF: 0.454 AC: 30803 AN: 67918

Other (OTH) AF: 0.434 AC: 913 AN: 2102

Alfa AF: 0.443 Hom.: 19051

Bravo AF: 0.466

Asia WGS AF: 0.585 AC: 2032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.46
PhyloP100		0.031
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs2293369; hg19: chr7-112720824;