rs3810711

Variant names:

• chrX-79170991-T-C
• rs3810711
• NM_032553.3:c.-17T>C

Your query was ambiguous. Multiple possible variants found:

• chrX-79170991-T-C
• chrX-79170991-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BP6_Very_Strong

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, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.578
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -12 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 VariationId is 1314977.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR174	NM_032553.3	c.-17T>C		5_prime_UTR_variant	Exon 3 of 3	ENST00000645147.2	NP_115942.1
GPR174	XM_047442579.1	c.-17T>C		5_prime_UTR_variant	Exon 3 of 3		XP_047298535.1
GPR174	XM_047442580.1	c.-17T>C		5_prime_UTR_variant	Exon 2 of 2		XP_047298536.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR174	ENST00000645147.2	c.-17T>C		5_prime_UTR_variant	Exon 3 of 3		NM_032553.3	ENSP00000494310.1

Frequencies

GnomAD3 genomes AF: 0.519 AC: 57541 AN: 110896 Hom.: 10893 Cov.: 23

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

GnomAD2 exomes AF: 0.514 AC: 73032 AN: 142218 AF XY: 0.538

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 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

African (AFR) AF: 0.415 AC: 10201 AN: 24609

American (AMR) AF: 0.290 AC: 8206 AN: 28292

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 7913 AN: 16278

East Asian (EAS) AF: 0.471 AC: 14047 AN: 29813

South Asian (SAS) AF: 0.522 AC: 24300 AN: 46590

European-Finnish (FIN) AF: 0.629 AC: 24261 AN: 38588

Middle Eastern (MID) AF: 0.600 AC: 2339 AN: 3897

European-Non Finnish (NFE) AF: 0.598 AC: 486820 AN: 814164

Other (OTH) AF: 0.560 AC: 24561 AN: 43866

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

African (AFR) AF: 0.415 AC: 12649 AN: 30502

American (AMR) AF: 0.422 AC: 4430 AN: 10506

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1248 AN: 2634

East Asian (EAS) AF: 0.401 AC: 1397 AN: 3485

South Asian (SAS) AF: 0.518 AC: 1377 AN: 2660

European-Finnish (FIN) AF: 0.640 AC: 3798 AN: 5935

Middle Eastern (MID) AF: 0.528 AC: 114 AN: 216

European-Non Finnish (NFE) AF: 0.594 AC: 31358 AN: 52828

Other (OTH) AF: 0.519 AC: 782 AN: 1506

Alfa AF: 0.561 Hom.: 37400

Bravo AF: 0.494

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 01, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	11
DANN	Benign	0.64
PhyloP100		0.58
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

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