7-113083393-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000424100.2(GPR85):​c.*216G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 539,658 control chromosomes in the GnomAD database, including 77 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 0.012 ( 21 hom., cov: 32)
Exomes 𝑓: 0.015 ( 56 hom. )

Consequence

GPR85
ENST00000424100.2 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.29
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=-0.57).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0123 (1880/152254) while in subpopulation NFE AF= 0.0203 (1379/68024). AF 95% confidence interval is 0.0194. There are 21 homozygotes in gnomad4. There are 849 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 21 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GPR85NM_001146267.2 linkuse as main transcriptc.*216G>A 3_prime_UTR_variant 3/3 ENST00000424100.2 NP_001139739.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GPR85ENST00000424100.2 linkuse as main transcriptc.*216G>A 3_prime_UTR_variant 3/31 NM_001146267.2 ENSP00000396763 P1
GPR85ENST00000297146.7 linkuse as main transcriptc.*216G>A 3_prime_UTR_variant 3/31 ENSP00000297146 P1
GPR85ENST00000449591.2 linkuse as main transcriptc.*216G>A 3_prime_UTR_variant 2/21 ENSP00000401178 P1
GPR85ENST00000610164.1 linkuse as main transcriptc.*216G>A 3_prime_UTR_variant, NMD_transcript_variant 2/35 ENSP00000476863

Frequencies

GnomAD3 genomes
AF:
0.0123
AC:
1878
AN:
152138
Hom.:
21
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00430
Gnomad AMI
AF:
0.0154
Gnomad AMR
AF:
0.0105
Gnomad ASJ
AF:
0.00922
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0106
Gnomad FIN
AF:
0.00264
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0203
Gnomad OTH
AF:
0.0167
GnomAD4 exome
AF:
0.0148
AC:
5739
AN:
387404
Hom.:
56
Cov.:
4
AF XY:
0.0149
AC XY:
3013
AN XY:
201988
show subpopulations
Gnomad4 AFR exome
AF:
0.00422
Gnomad4 AMR exome
AF:
0.00973
Gnomad4 ASJ exome
AF:
0.0106
Gnomad4 EAS exome
AF:
0.0000722
Gnomad4 SAS exome
AF:
0.0102
Gnomad4 FIN exome
AF:
0.00434
Gnomad4 NFE exome
AF:
0.0194
Gnomad4 OTH exome
AF:
0.0140
GnomAD4 genome
AF:
0.0123
AC:
1880
AN:
152254
Hom.:
21
Cov.:
32
AF XY:
0.0114
AC XY:
849
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.00428
Gnomad4 AMR
AF:
0.0105
Gnomad4 ASJ
AF:
0.00922
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0110
Gnomad4 FIN
AF:
0.00264
Gnomad4 NFE
AF:
0.0203
Gnomad4 OTH
AF:
0.0166
Alfa
AF:
0.0162
Hom.:
4
Bravo
AF:
0.0125
Asia WGS
AF:
0.00866
AC:
30
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.57
CADD
Benign
11
DANN
Benign
0.67

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

Publications

LitVar

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

Other links and lift over

dbSNP: rs56320353; hg19: chr7-112723448; API