chrX-130381097-G-T

Position:

• chrX-130381097-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178471.3(GPR119):​c.*1459C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 109,574 control chromosomes in the GnomAD database, including 6,295 homozygotes. There are 12,250 hemizygotes in GnomAD. 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 0.40 (6295 hom., 12250 hem., cov: 21)
• Consequence: GPR119 NM_178471.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPR119	NM_178471.3	c.*1459C>A		3_prime_UTR_variant	2/2	ENST00000682440.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPR119	ENST00000682440.1	c.*1459C>A		3_prime_UTR_variant	2/2		NM_178471.3	P1

Frequencies

GnomAD3 genomes AF: 0.396 AC: 43380 AN: 109532 Hom.: 6299 Cov.: 21 AF XY: 0.384 AC XY: 12236 AN XY: 31898

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.396 AC: 43369 AN: 109574 Hom.: 6295 Cov.: 21 AF XY: 0.383 AC XY: 12250 AN XY: 31950

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.385

Alfa AF: 0.408 Hom.: 4317

Bravo AF: 0.397

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.23
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5932754; hg19: chrX-129515071;