chr7-113080769-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0310
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GPR85ENST00000297146.7 linkuse as main transcriptc.*2840G>T 3_prime_UTR_variant 3/31 ENSP00000297146 P1
GPR85ENST00000610164.1 linkuse as main transcriptc.*542-255G>T intron_variant, NMD_transcript_variant 5 ENSP00000476863

Frequencies

GnomAD3 genomes
AF:
0.460
AC:
69840
AN:
151684
Hom.:
16957
Cov.:
31
show subpopulations
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
show subpopulations
Gnomad4 NFE exome
AF:
0.500
GnomAD4 genome
AF:
0.460
AC:
69897
AN:
151802
Hom.:
16974
Cov.:
31
AF XY:
0.466
AC XY:
34530
AN XY:
74156
show subpopulations
Gnomad4 AFR
AF:
0.385
Gnomad4 AMR
AF:
0.550
Gnomad4 ASJ
AF:
0.438
Gnomad4 EAS
AF:
0.917
Gnomad4 SAS
AF:
0.340
Gnomad4 FIN
AF:
0.529
Gnomad4 NFE
AF:
0.454
Gnomad4 OTH
AF:
0.434
Alfa
AF:
0.440
Hom.:
14182
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

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2293369; hg19: chr7-112720824; API