rs4829716

Variant names:

• chrX-130379957-G-A
• rs4829716
• NM_178471.3:c.*2599C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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
• Publications: 3 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR119	NM_178471.3	c.*2599C>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000682440.1	NP_848566.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR119	ENST00000682440.1	c.*2599C>T		3_prime_UTR_variant	Exon 2 of 2		NM_178471.3	ENSP00000508182.1

Frequencies

GnomAD3 genomes AF: 0.609 AC: 67773 AN: 111332 Hom.: 15611 Cov.: 24

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

African (AFR) AF: 0.816 AC: 25078 AN: 30718

American (AMR) AF: 0.472 AC: 4954 AN: 10493

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1453 AN: 2649

East Asian (EAS) AF: 0.376 AC: 1324 AN: 3521

South Asian (SAS) AF: 0.469 AC: 1252 AN: 2670

European-Finnish (FIN) AF: 0.427 AC: 2525 AN: 5916

Middle Eastern (MID) AF: 0.610 AC: 133 AN: 218

European-Non Finnish (NFE) AF: 0.564 AC: 29884 AN: 53001

Other (OTH) AF: 0.572 AC: 874 AN: 1527

Alfa AF: 0.580 Hom.: 39123

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
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs4829716; hg19: chrX-129513931;