7-113083466-A-T

Variant names:

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

Variant summary

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

The NM_001146267.2(GPR85):​c.*143T>A variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.06 in 744,784 control chromosomes in the GnomAD database, including 1,529 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 0.058 (308 hom., cov: 32)
  • Exomes 𝑓: 0.060 (1221 hom.)
• Consequence: GPR85 NM_001146267.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.96
• Publications: 7 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=-0.49).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0652 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.0583 AC: 8864 AN: 152128 Hom.: 309 Cov.: 32

Gnomad AFR AF: 0.0599

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0687

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.0469

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0595

Gnomad OTH AF: 0.0727

GnomAD4 exome AF: 0.0605 AC: 35842 AN: 592538 Hom.: 1221 Cov.: 8 AF XY: 0.0611 AC XY: 19076 AN XY: 312298

African (AFR) AF: 0.0650 AC: 1014 AN: 15602

American (AMR) AF: 0.0798 AC: 2105 AN: 26378

Ashkenazi Jewish (ASJ) AF: 0.0535 AC: 800 AN: 14954

East Asian (EAS) AF: 0.000227 AC: 8 AN: 35304

South Asian (SAS) AF: 0.0783 AC: 4005 AN: 51136

European-Finnish (FIN) AF: 0.0485 AC: 2172 AN: 44772

Middle Eastern (MID) AF: 0.0888 AC: 195 AN: 2196

European-Non Finnish (NFE) AF: 0.0635 AC: 23565 AN: 371326

Other (OTH) AF: 0.0641 AC: 1978 AN: 30870

GnomAD4 genome AF: 0.0582 AC: 8866 AN: 152246 Hom.: 308 Cov.: 32 AF XY: 0.0583 AC XY: 4338 AN XY: 74440

African (AFR) AF: 0.0598 AC: 2487 AN: 41562

American (AMR) AF: 0.0686 AC: 1048 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5188

South Asian (SAS) AF: 0.0711 AC: 343 AN: 4822

European-Finnish (FIN) AF: 0.0469 AC: 497 AN: 10602

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0594 AC: 4043 AN: 68008

Other (OTH) AF: 0.0714 AC: 151 AN: 2114

Alfa AF: 0.0555 Hom.: 32

Bravo AF: 0.0604

Asia WGS AF: 0.0280 AC: 97 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	17
DANN	Benign	0.71
PhyloP100		4.0
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: rs870266; hg19: chr7-112723521;