rs4829716

chrX-130379957-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_178471.3(GPR119):c.*2599C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.61 (15609 hom., 19742 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: GPR119 NM_178471.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS2: High Homozygotes in GnomAd at 15611 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPR119	NM_178471.3	c.*2599C>T		3_prime_UTR_variant	2/2	ENST00000682440.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPR119	ENST00000682440.1	c.*2599C>T		3_prime_UTR_variant	2/2		NM_178471.3	P1

Frequencies

GnomAD3 genomes AF: 0.609 AC: 67773 AN: 111332 Hom.: 15611 Cov.: 24 AF XY: 0.587 AC XY: 19700 AN XY: 33534

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.580

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.609 AC: 67795 AN: 111386 Hom.: 15609 Cov.: 24 AF XY: 0.588 AC XY: 19742 AN XY: 33598

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.572

Alfa AF: 0.575 Hom.: 29096

Bravo AF: 0.621

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.4
Dann	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4829716; hg19: chrX-129513931;