Variant chr3-120167296-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_153002.3(GPR156):c.2181G>T(p.Trp727Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

GPR156
NM_153002.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.508

Variant links:

Genes affected

GPR156 (HGNC:20844): (G protein-coupled receptor 156) G protein-coupled receptors (GPCRs) are a large superfamily of cell surface receptors characterized by 7 helical transmembrane domains, together with N-terminal extracellular and C-terminal intracellular domains.[supplied by OMIM, Mar 2008]

GPR156 links:

LOC105374065 (HGNC:):

LOC105374065 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.06618488).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPR156	NM_153002.3 linkuse as main transcript	c.2181G>T	p.Trp727Cys	missense_variant	10/10	ENST00000464295.6	NP_694547.2	Q8NFN8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
GPR156	ENST00000464295.6 linkuse as main transcript	c.2181G>T	p.Trp727Cys	missense_variant	10/10	5	NM_153002.3	ENSP00000417261.1	Q8NFN8-1
GPR156	ENST00000461057.1 linkuse as main transcript	c.2169G>T	p.Trp723Cys	missense_variant	9/9	1		ENSP00000418758.1	Q8NFN8-2
GPR156	ENST00000495912.5 linkuse as main transcript	n.*1244G>T		non_coding_transcript_exon_variant	4/4	5		ENSP00000417191.1	F8WAW3
GPR156	ENST00000495912.5 linkuse as main transcript	n.*1244G>T		3_prime_UTR_variant	4/4	5		ENSP00000417191.1	F8WAW3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1461164

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

726832

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

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 10, 2024

The c.2181G>T (p.W727C) alteration is located in exon 9 (coding exon 9) of the GPR156 gene. This alteration results from a G to T substitution at nucleotide position 2181, causing the tryptophan (W) at amino acid position 727 to be replaced by a cysteine (C). 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

0.13

BayesDel_addAF

Benign

-0.26

BayesDel_noAF

Benign

-0.61

CADD

Benign

5.6

DANN

Benign

0.45

DEOGEN2

Benign

0.00062

T;T;.

Eigen

Benign

-0.90

Eigen_PC

Benign

-0.96

FATHMM_MKL

Benign

0.020

LIST_S2

Benign

0.49

T;.;T

M_CAP

Benign

0.0052

MetaRNN

Benign

0.066

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.0

N;N;.

PrimateAI

Benign

0.25

PROVEAN

Benign

-0.72

N;N;N

REVEL

Benign

0.0040

Sift

Uncertain

0.019

D;D;D

Sift4G

Benign

0.16

T;T;T

Polyphen

0.37

B;B;.

Vest4

0.16

MutPred

0.22

Loss of glycosylation at S732 (P = 0.033);Loss of glycosylation at S732 (P = 0.033);.;

MVP

0.048

MPC

0.57

ClinPred

0.074

GERP RS

0.30

Varity_R

0.11

gMVP

0.12

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