rs3810711

chrX-79170991-T-CchrX-79170991-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_032553.3(GPR174):c.-17T>C 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 (10888 hom., 17184 hem., cov: 23)
  • Exomes 𝑓: 0.58 (120568 hom. 192364 hem.)
  • Failed GnomAD Quality Control
• Consequence: GPR174 NM_032553.3 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.578

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant X-79170991-T-C is Benign according to our data. Variant chrX-79170991-T-C is described in ClinVar as [Benign]. Clinvar id is 1314977.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd at 10893 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPR174	NM_032553.3	c.-17T>C		5_prime_UTR_variant	3/3	ENST00000645147.2
GPR174	XM_047442579.1	c.-17T>C		5_prime_UTR_variant	3/3
GPR174	XM_047442580.1	c.-17T>C		5_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPR174	ENST00000645147.2	c.-17T>C		5_prime_UTR_variant	3/3		NM_032553.3	P1

Frequencies

GnomAD3 genomes AF: 0.519 AC: 57541 AN: 110896 Hom.: 10893 Cov.: 23 AF XY: 0.518 AC XY: 17167 AN XY: 33172

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.521

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.518

GnomAD3 exomes AF: 0.514 AC: 73032 AN: 142218 Hom.: 13335 AF XY: 0.538 AC XY: 24045 AN XY: 44734

Gnomad AFR exome AF: 0.412

Gnomad AMR exome AF: 0.274

Gnomad ASJ exome AF: 0.487

Gnomad EAS exome AF: 0.397

Gnomad SAS exome AF: 0.544

Gnomad FIN exome AF: 0.628

Gnomad NFE exome AF: 0.601

Gnomad OTH exome AF: 0.560

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.576 AC: 602648 AN: 1046097 Hom.: 120568 Cov.: 28 AF XY: 0.575 AC XY: 192364 AN XY: 334475

Gnomad4 AFR exome AF: 0.415

Gnomad4 AMR exome AF: 0.290

Gnomad4 ASJ exome AF: 0.486

Gnomad4 EAS exome AF: 0.471

Gnomad4 SAS exome AF: 0.522

Gnomad4 FIN exome AF: 0.629

Gnomad4 NFE exome AF: 0.598

Gnomad4 OTH exome AF: 0.560

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.519 AC: 57551 AN: 110948 Hom.: 10888 Cov.: 23 AF XY: 0.517 AC XY: 17184 AN XY: 33234

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.519

Alfa AF: 0.573 Hom.: 28894

Bravo AF: 0.494

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 01, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	11
Dann	Benign	0.64

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

Other links and lift over

dbSNP: rs3810711; hg19: chrX-78426488; COSMIC: COSV52131355;