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GeneBe

7-113084092-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001146267.2(GPR85):c.630C>T(p.His210=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00364 in 1,614,038 control chromosomes in the GnomAD database, including 195 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.020 ( 110 hom., cov: 32)
Exomes 𝑓: 0.0020 ( 85 hom. )

Consequence

GPR85
NM_001146267.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.550
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 -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-113084092-G-A is Benign according to our data. Variant chr7-113084092-G-A is described in ClinVar as [Benign]. Clinvar id is 768195.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.55 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0678 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GPR85NM_001146267.2 linkuse as main transcriptc.630C>T p.His210= synonymous_variant 3/3 ENST00000424100.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GPR85ENST00000424100.2 linkuse as main transcriptc.630C>T p.His210= synonymous_variant 3/31 NM_001146267.2 P1
GPR85ENST00000297146.7 linkuse as main transcriptc.630C>T p.His210= synonymous_variant 3/31 P1
GPR85ENST00000449591.2 linkuse as main transcriptc.630C>T p.His210= synonymous_variant 2/21 P1
GPR85ENST00000610164.1 linkuse as main transcriptc.630C>T p.His210= synonymous_variant, NMD_transcript_variant 2/35

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0199
AC:
3030
AN:
152054
Hom.:
111
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0701
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00550
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000827
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.000103
Gnomad OTH
AF:
0.0148
GnomAD3 exomes
AF:
0.00524
AC:
1317
AN:
251450
Hom.:
48
AF XY:
0.00385
AC XY:
523
AN XY:
135890
show subpopulations
Gnomad AFR exome
AF:
0.0729
Gnomad AMR exome
AF:
0.00298
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000980
Gnomad FIN exome
AF:
0.0000925
Gnomad NFE exome
AF:
0.000114
Gnomad OTH exome
AF:
0.00179
GnomAD4 exome
AF:
0.00195
AC:
2856
AN:
1461866
Hom.:
85
Cov.:
32
AF XY:
0.00168
AC XY:
1223
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.0719
Gnomad4 AMR exome
AF:
0.00315
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000162
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.0000279
Gnomad4 OTH exome
AF:
0.00417
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0199
AC:
3027
AN:
152172
Hom.:
110
Cov.:
32
AF XY:
0.0189
AC XY:
1409
AN XY:
74416
show subpopulations
Gnomad4 AFR
AF:
0.0699
Gnomad4 AMR
AF:
0.00550
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000103
Gnomad4 OTH
AF:
0.0147
Alfa
AF:
0.0112
Hom.:
26
Bravo
AF:
0.0224
Asia WGS
AF:
0.00491
AC:
17
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeApr 16, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
Cadd
Benign
5.5
Dann
Benign
0.60

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: rs28392728; hg19: chr7-112724147; COSMIC: COSV99775206; COSMIC: COSV99775206; API