chrX-130380449-C-T

Variant names:

• chrX-130380449-C-T
• rs4830188
• NM_178471.3:c.*2107G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178471.3(GPR119):​c.*2107G>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 0.394 in 111,592 control chromosomes in the GnomAD database, including 6,292 homozygotes. There are 12,828 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 0.39 (6292 hom., 12828 hem., cov: 23)
• Consequence: GPR119 NM_178471.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 2 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR119	NM_178471.3	c.*2107G>A		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.*2107G>A		3_prime_UTR_variant	Exon 2 of 2		NM_178471.3	ENSP00000508182.1

Frequencies

GnomAD3 genomes AF: 0.394 AC: 43970 AN: 111537 Hom.: 6296 Cov.: 23

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.394 AC: 43958 AN: 111592 Hom.: 6292 Cov.: 23 AF XY: 0.379 AC XY: 12828 AN XY: 33830

African (AFR) AF: 0.337 AC: 10370 AN: 30763

American (AMR) AF: 0.362 AC: 3825 AN: 10565

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1075 AN: 2641

East Asian (EAS) AF: 0.346 AC: 1220 AN: 3526

South Asian (SAS) AF: 0.408 AC: 1094 AN: 2684

European-Finnish (FIN) AF: 0.326 AC: 1955 AN: 6002

Middle Eastern (MID) AF: 0.437 AC: 94 AN: 215

European-Non Finnish (NFE) AF: 0.444 AC: 23513 AN: 52994

Other (OTH) AF: 0.377 AC: 573 AN: 1521

Alfa AF: 0.427 Hom.: 22403

Bravo AF: 0.396

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.65
DANN	Benign	0.36
PhyloP100		-0.071

Splicing

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

Other links and lift over

dbSNP: rs4830188; hg19: chrX-129514423;