rs56080411

Positions:

• chr7-113080660-T-C

Variant summary

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

The ENST00000297146.7(GPR85):​c.*2949A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,196 control chromosomes in the GnomAD database, including 1,838 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 0.15 (1838 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GPR85 ENST00000297146.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.558

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=-0.52).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPR85	ENST00000297146.7	c.*2949A>G		3_prime_UTR_variant	3/3	1		ENSP00000297146	P1
GPR85	ENST00000610164.1	c.*542-146A>G		intron_variant, NMD_transcript_variant		5		ENSP00000476863

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22723 AN: 152078 Hom.: 1835 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.0182

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.148

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 AFR exome AF: 0.00

GnomAD4 genome AF: 0.149 AC: 22750 AN: 152196 Hom.: 1838 Cov.: 32 AF XY: 0.150 AC XY: 11156 AN XY: 74426

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.0182

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.147

Alfa AF: 0.156 Hom.: 454

Bravo AF: 0.146

Asia WGS AF: 0.115 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	18
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.12		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: rs56080411; hg19: chr7-112720715;