Variant 12-54363128-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_020370.3(GPR84):c.724G>C(p.Asp242His) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

GPR84
NM_020370.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.63

Variant links:

Genes affected

GPR84 (HGNC:4535): (G protein-coupled receptor 84) Predicted to enable urotensin II receptor activity. Predicted to be involved in neuropeptide signaling pathway. Part of receptor complex. [provided by Alliance of Genome Resources, Apr 2022]

GPR84 links:

GPR84-AS1 (HGNC:):

GPR84-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPR84	NM_020370.3 linkuse as main transcript	c.724G>C	p.Asp242His	missense_variant	2/2	ENST00000267015.4	NP_065103.1	Q9NQS5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
GPR84	ENST00000267015.4 linkuse as main transcript	c.724G>C	p.Asp242His	missense_variant	2/2	1	NM_020370.3	ENSP00000267015.3	Q9NQS5
GPR84	ENST00000551809.1 linkuse as main transcript	c.724G>C	p.Asp242His	missense_variant	1/1	6		ENSP00000450310.1	Q9NQS5
GPR84-AS1	ENST00000550474.5 linkuse as main transcript	n.47+9421C>G		intron_variant		4
GPR84-AS1	ENST00000552785.1 linkuse as main transcript	n.105+9232C>G		intron_variant		4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 03, 2024

The c.724G>C (p.D242H) alteration is located in exon 2 (coding exon 1) of the GPR84 gene. This alteration results from a G to C substitution at nucleotide position 724, causing the aspartic acid (D) at amino acid position 242 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

BayesDel_addAF

Uncertain

0.11

BayesDel_noAF

Uncertain

-0.080

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.013

T;T

Eigen

Uncertain

0.62

Eigen_PC

Uncertain

0.59

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.75

.;T

M_CAP

Benign

0.024

MetaRNN

Uncertain

0.43

T;T

MetaSVM

Benign

-0.42

MutationAssessor

Uncertain

2.7

M;M

PrimateAI

Uncertain

0.54

PROVEAN

Benign

-0.93

N;N

REVEL

Benign

0.20

Sift

Benign

0.030

D;D

Sift4G

Pathogenic

0.0

D;D

Polyphen

1.0

D;D

Vest4

0.57

MutPred

0.46

Gain of helix (P = 0.062);Gain of helix (P = 0.062);

MVP

0.84

MPC

0.72

ClinPred

0.95

GERP RS

5.0

Varity_R

0.23

gMVP

0.42

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

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over