Variant chrX-79170974-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The NM_032553.3(GPR174):c.-34C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.52 ( 10748 hom., 17057 hem., cov: 23)

Exomes 𝑓: 0.57 ( 116135 hom. 177721 hem. )

Failed GnomAD Quality Control

Consequence

GPR174
NM_032553.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0140

Variant links:

Genes affected

GPR174 (HGNC:30245): (G protein-coupled receptor 174) This gene encodes a protein belonging to the G protein-coupled receptor superfamily. These proteins are characterized by the presence of seven alpha-helical transmembrane domains, and they activate or interact with various endogenous or exogenous ligands, including neurotransmitters, hormones, and odorant and taste substances. This family member is classified as an orphan receptor because the cognate ligand has not been identified. [provided by RefSeq, Sep 2011]

GPR174 links:

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=-0.88).

BP6

Variant X-79170974-C-T is Benign according to our data. Variant chrX-79170974-C-T is described in ClinVar as [Benign]. Clinvar id is 1314975.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
GPR174	NM_032553.3 linkuse as main transcript	c.-34C>T	5_prime_UTR_variant	3/3	ENST00000645147.2	NP_115942.1	Q9BXC1
GPR174	XM_047442579.1 linkuse as main transcript	c.-34C>T	5_prime_UTR_variant	3/3		XP_047298535.1
GPR174	XM_047442580.1 linkuse as main transcript	c.-34C>T	5_prime_UTR_variant	2/2		XP_047298536.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPR174	ENST00000645147.2 linkuse as main transcript	c.-34C>T		5_prime_UTR_variant	3/3		NM_032553.3	ENSP00000494310.1		Q9BXC1

Frequencies

GnomAD3 genomes

AF:

0.515

AC:

57160

AN:

110944

Hom.:

10752

Cov.:

AF XY:

0.513

AC XY:

17038

AN XY:

33198

show subpopulations

Gnomad AFR

AF:

0.415

Gnomad AMI

AF:

0.590

Gnomad AMR

AF:

0.421

Gnomad ASJ

AF:

0.471

Gnomad EAS

AF:

0.402

Gnomad SAS

AF:

0.416

Gnomad FIN

AF:

0.642

Gnomad MID

AF:

0.523

Gnomad NFE

AF:

0.591

Gnomad OTH

AF:

0.518

GnomAD3 exomes

AF:

0.501

AC:

67677

AN:

135092

Hom.:

12241

AF XY:

0.516

AC XY:

21729

AN XY:

42118

show subpopulations

Gnomad AFR exome

AF:

0.409

Gnomad AMR exome

AF:

0.272

Gnomad ASJ exome

AF:

0.479

Gnomad EAS exome

AF:

0.395

Gnomad SAS exome

AF:

0.435

Gnomad FIN exome

AF:

0.625

Gnomad NFE exome

AF:

0.594

Gnomad OTH exome

AF:

0.547

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.566

AC:

577287

AN:

1019570

Hom.:

116135

Cov.:

AF XY:

0.558

AC XY:

177721

AN XY:

318320

show subpopulations

Gnomad4 AFR exome

AF:

0.412

Gnomad4 AMR exome

AF:

0.292

Gnomad4 ASJ exome

AF:

0.482

Gnomad4 EAS exome

AF:

0.470

Gnomad4 SAS exome

AF:

0.425

Gnomad4 FIN exome

AF:

0.628

Gnomad4 NFE exome

AF:

0.591

Gnomad4 OTH exome

AF:

0.549

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.515

AC:

57173

AN:

110997

Hom.:

10748

Cov.:

AF XY:

0.513

AC XY:

17057

AN XY:

33261

show subpopulations

Gnomad4 AFR

AF:

0.415

Gnomad4 AMR

AF:

0.420

Gnomad4 ASJ

AF:

0.471

Gnomad4 EAS

AF:

0.403

Gnomad4 SAS

AF:

0.415

Gnomad4 FIN

AF:

0.642

Gnomad4 NFE

AF:

0.591

Gnomad4 OTH

AF:

0.520

Alfa

AF:

0.560

Hom.:

28914

Bravo

AF:

0.492

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 01, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

8.6

DANN

Benign

0.70

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over