chr7-113080660-T-C

Variant names:

• chr7-113080660-T-C
• rs56080411
• ENST00000297146.7:c.*2949A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.52).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR85	ENST00000297146.7	c.*2949A>G		3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000297146.2
GPR85	ENST00000610164.1	n.*542-146A>G		intron_variant	Intron 2 of 2	5		ENSP00000476863.1

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

African (AFR) AF: 0.00 AC: 0 AN: 2

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.144 AC: 5959 AN: 41518

American (AMR) AF: 0.127 AC: 1938 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3470

East Asian (EAS) AF: 0.0182 AC: 94 AN: 5166

South Asian (SAS) AF: 0.225 AC: 1084 AN: 4822

European-Finnish (FIN) AF: 0.146 AC: 1551 AN: 10614

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11212 AN: 68002

Other (OTH) AF: 0.147 AC: 310 AN: 2108

Alfa AF: 0.151 Hom.: 881

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
PhyloP100		0.56
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs56080411; hg19: chr7-112720715;