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GeneBe

X-130385307-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_178471.3(GPR119):c.141G>A(p.Leu47=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000197 in 1,210,623 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 84 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00018 ( 0 hom., 2 hem., cov: 23)
Exomes 𝑓: 0.00020 ( 0 hom. 82 hem. )

Consequence

GPR119
NM_178471.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.110
Variant links:
Genes affected
GPR119 (HGNC:19060): (G protein-coupled receptor 119) This gene encodes a member of the rhodopsin subfamily of G-protein-coupled receptors that is expressed in the pancreas and gastrointestinal tract. The encoded protein is activated by lipid amides including lysophosphatidylcholine and oleoylethanolamide and may be involved in glucose homeostasis. This protein is a potential drug target in the treatment of type 2 diabetes.[provided by RefSeq, Jan 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant X-130385307-C-T is Benign according to our data. Variant chrX-130385307-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2661438.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.11 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Hemizygotes in GnomAd at 2 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GPR119NM_178471.3 linkuse as main transcriptc.141G>A p.Leu47= synonymous_variant 1/2 ENST00000682440.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GPR119ENST00000682440.1 linkuse as main transcriptc.141G>A p.Leu47= synonymous_variant 1/2 NM_178471.3 P1
GPR119ENST00000276218.4 linkuse as main transcriptc.141G>A p.Leu47= synonymous_variant 1/1 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000178
AC:
20
AN:
112425
Hom.:
0
Cov.:
23
AF XY:
0.0000578
AC XY:
2
AN XY:
34583
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00377
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00420
Gnomad NFE
AF:
0.000169
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000366
AC:
67
AN:
183081
Hom.:
0
AF XY:
0.000369
AC XY:
25
AN XY:
67665
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000219
Gnomad ASJ exome
AF:
0.00590
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000159
Gnomad OTH exome
AF:
0.000885
GnomAD4 exome
AF:
0.000199
AC:
219
AN:
1098198
Hom.:
0
Cov.:
31
AF XY:
0.000226
AC XY:
82
AN XY:
363552
show subpopulations
Gnomad4 AFR exome
AF:
0.000114
Gnomad4 AMR exome
AF:
0.000227
Gnomad4 ASJ exome
AF:
0.00573
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000739
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000689
Gnomad4 OTH exome
AF:
0.000694
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000178
AC:
20
AN:
112425
Hom.:
0
Cov.:
23
AF XY:
0.0000578
AC XY:
2
AN XY:
34583
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00377
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000169
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000998
Hom.:
6
Bravo
AF:
0.000223
EpiCase
AF:
0.000545
EpiControl
AF:
0.000296

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2022GPR119: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.45
Cadd
Benign
8.6
Dann
Benign
0.75

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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.

Other links and lift over

dbSNP: rs143653619; hg19: chrX-129519281; API