Variant rs5931046 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_054021.2(GPR101):c.1127T>C(p.Leu376Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 1,207,840 control chromosomes in the GnomAD database, including 10,271 homozygotes. There are 64,138 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.17 ( 1231 hom., 5335 hem., cov: 22)

Exomes 𝑓: 0.16 ( 9040 hom. 58803 hem. )

Consequence

GPR101
NM_054021.2 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.524

Variant links:

Genes affected

GPR101 (HGNC:14963): (G protein-coupled receptor 101) The protein encoded by this gene is an orphan G protein-coupled receptor of unknown function. The encoded protein is a member of a family of proteins that contain seven transmembrane domains and transduce extracellular signals through heterotrimeric G proteins. [provided by RefSeq, Sep 2011]

GPR101 links:

ENSG00000291054 (HGNC:):

ENSG00000291054 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0038969219).

BP6

Variant X-137030548-A-G is Benign according to our data. Variant chrX-137030548-A-G is described in ClinVar as [Benign]. Clinvar id is 1563029.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPR101	NM_054021.2 linkuse as main transcript	c.1127T>C	p.Leu376Pro	missense_variant	2/2	ENST00000651716.2	NP_473362.1	Q96P66

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPR101	ENST00000651716.2 linkuse as main transcript	c.1127T>C	p.Leu376Pro	missense_variant	2/2		NM_054021.2	ENSP00000498972.1		Q96P66
ENSG00000291054	ENST00000693626.2 linkuse as main transcript	n.394-29977A>G		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.172

AC:

18950

AN:

110220

Hom.:

1230

Cov.:

AF XY:

0.164

AC XY:

5335

AN XY:

32548

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.187

Gnomad AMR

AF:

0.131

Gnomad ASJ

AF:

0.186

Gnomad EAS

AF:

0.114

Gnomad SAS

AF:

0.297

Gnomad FIN

AF:

0.129

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.149

Gnomad OTH

AF:

0.164

GnomAD3 exomes

AF:

0.168

AC:

30519

AN:

181902

Hom.:

1755

AF XY:

0.176

AC XY:

11715

AN XY:

66386

show subpopulations

Gnomad AFR exome

AF:

0.235

Gnomad AMR exome

AF:

0.111

Gnomad ASJ exome

AF:

0.192

Gnomad EAS exome

AF:

0.125

Gnomad SAS exome

AF:

0.317

Gnomad FIN exome

AF:

0.138

Gnomad NFE exome

AF:

0.152

Gnomad OTH exome

AF:

0.182

GnomAD4 exome

AF:

0.157

AC:

171861

AN:

1097567

Hom.:

9040

Cov.:

AF XY:

0.162

AC XY:

58803

AN XY:

362943

show subpopulations

Gnomad4 AFR exome

AF:

0.238

Gnomad4 AMR exome

AF:

0.115

Gnomad4 ASJ exome

AF:

0.193

Gnomad4 EAS exome

AF:

0.106

Gnomad4 SAS exome

AF:

0.302

Gnomad4 FIN exome

AF:

0.138

Gnomad4 NFE exome

AF:

0.147

Gnomad4 OTH exome

AF:

0.170

GnomAD4 genome

AF:

0.172

AC:

18950

AN:

110273

Hom.:

1231

Cov.:

AF XY:

0.164

AC XY:

5335

AN XY:

32611

show subpopulations

Gnomad4 AFR

AF:

0.229

Gnomad4 AMR

AF:

0.131

Gnomad4 ASJ

AF:

0.186

Gnomad4 EAS

AF:

0.114

Gnomad4 SAS

AF:

0.292

Gnomad4 FIN

AF:

0.129

Gnomad4 NFE

AF:

0.149

Gnomad4 OTH

AF:

0.170

Alfa

AF:

0.157

Hom.:

10856

Bravo

AF:

0.174

TwinsUK

AF:

0.159

AC:

589

ALSPAC

AF:

0.150

AC:

432

ESP6500AA

AF:

0.214

AC:

820

ESP6500EA

AF:

0.148

AC:

993

ExAC

AF:

0.175

AC:

21192

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.59

BayesDel_noAF

Benign

-0.48

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0058

FATHMM_MKL

Benign

0.063

LIST_S2

Benign

0.42

MetaRNN

Benign

0.0039

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.5

PrimateAI

Benign

0.39

PROVEAN

Benign

-0.94

REVEL

Benign

0.095

Sift

Benign

0.12

Sift4G

Uncertain

0.054

Polyphen

0.77

Vest4

0.10

MPC

1.6

ClinPred

0.027

GERP RS

2.8

Varity_R

0.17

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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