Variant rs1800437 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000164.4(GIPR):c.1060G>C(p.Glu354Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 1,611,060 control chromosomes in the GnomAD database, including 30,514 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.17 ( 2479 hom., cov: 32)

Exomes 𝑓: 0.19 ( 28035 hom. )

Consequence

GIPR
NM_000164.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.82

Variant links:

Genes affected

GIPR (HGNC:4271): (gastric inhibitory polypeptide receptor) This gene encodes a G-protein coupled receptor for gastric inhibitory polypeptide (GIP), which was originally identified as an activity in gut extracts that inhibited gastric acid secretion and gastrin release, but subsequently was demonstrated to stimulate insulin release in the presence of elevated glucose. Mice lacking this gene exhibit higher blood glucose levels with impaired initial insulin response after oral glucose load. Defect in this gene thus may contribute to the pathogenesis of diabetes. [provided by RefSeq, Oct 2011]

GIPR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GIPR	NM_000164.4 linkuse as main transcript	c.1060G>C	p.Glu354Gln	missense_variant	12/14	ENST00000590918.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIPR	ENST00000590918.6 linkuse as main transcript	c.1060G>C	p.Glu354Gln	missense_variant	12/14	1	NM_000164.4	P2	P48546-1

Frequencies

GnomAD3 genomes

AF:

0.175

AC:

26534

AN:

151948

Hom.:

2483

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.132

Gnomad ASJ

AF:

0.295

Gnomad EAS

AF:

0.198

Gnomad SAS

AF:

0.151

Gnomad FIN

AF:

0.228

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.197

GnomAD3 exomes

AF:

0.182

AC:

44732

AN:

245834

Hom.:

4273

AF XY:

0.184

AC XY:

24509

AN XY:

133338

show subpopulations

Gnomad AFR exome

AF:

0.110

Gnomad AMR exome

AF:

0.0970

Gnomad ASJ exome

AF:

0.291

Gnomad EAS exome

AF:

0.208

Gnomad SAS exome

AF:

0.141

Gnomad FIN exome

AF:

0.233

Gnomad NFE exome

AF:

0.205

Gnomad OTH exome

AF:

0.196

GnomAD4 exome

AF:

0.193

AC:

281107

AN:

1458994

Hom.:

28035

Cov.:

AF XY:

0.192

AC XY:

139375

AN XY:

725728

show subpopulations

Gnomad4 AFR exome

AF:

0.111

Gnomad4 AMR exome

AF:

0.102

Gnomad4 ASJ exome

AF:

0.282

Gnomad4 EAS exome

AF:

0.215

Gnomad4 SAS exome

AF:

0.144

Gnomad4 FIN exome

AF:

0.242

Gnomad4 NFE exome

AF:

0.198

Gnomad4 OTH exome

AF:

0.189

GnomAD4 genome

AF:

0.175

AC:

26536

AN:

152066

Hom.:

2479

Cov.:

AF XY:

0.173

AC XY:

12886

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.115

Gnomad4 AMR

AF:

0.132

Gnomad4 ASJ

AF:

0.295

Gnomad4 EAS

AF:

0.199

Gnomad4 SAS

AF:

0.151

Gnomad4 FIN

AF:

0.228

Gnomad4 NFE

AF:

0.206

Gnomad4 OTH

AF:

0.198

Alfa

AF:

0.204

Hom.:

2519

Bravo

AF:

0.165

TwinsUK

AF:

0.200

AC:

741

ALSPAC

AF:

0.196

AC:

754

ESP6500AA

AF:

0.113

AC:

500

ESP6500EA

AF:

0.203

AC:

1750

ExAC

AF:

0.183

AC:

22260

Asia WGS

AF:

0.165

AC:

574

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.46

BayesDel_addAF

Benign

-0.59

BayesDel_noAF

Benign

-0.48

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.38

T;.;.

Eigen

Uncertain

0.45

Eigen_PC

Uncertain

0.36

FATHMM_MKL

Uncertain

0.79

LIST_S2

Uncertain

0.89

D;D;D

MetaRNN

Benign

0.0018

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.6

M;M;.

MutationTaster

Benign

0.021

P;P;P

PrimateAI

Pathogenic

0.81

PROVEAN

Uncertain

-2.4

.;N;D

REVEL

Benign

0.17

Sift

Uncertain

0.0040

.;D;D

Sift4G

Uncertain

0.014

D;D;D

Polyphen

1.0

D;D;.

Vest4

0.15

MPC

0.88

ClinPred

0.023

GERP RS

3.1

Varity_R

0.61

gMVP

0.57

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.43

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.43

Position offset: 3

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over