rs2315598

Positions:

• chr2-132520181-T-C

Variant summary

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

The NM_001508.3(GPR39):​c.856+102283T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 152,046 control chromosomes in the GnomAD database, including 16,521 homozygotes. 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 0.44 (16521 hom., cov: 32)
• Consequence: GPR39 NM_001508.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58

Genes affected

GPR39 (HGNC:4496): (G protein-coupled receptor 39) This gene is a member of the ghrelin receptor family and encodes a rhodopsin-type G-protein-coupled receptor (GPCR). The encoded protein is involved in zinc-dependent signaling in epithelial tissue in intestines, prostate and salivary glands. The protein may also be involved in the pathophysiology of depression. [provided by RefSeq, Jun 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPR39	NM_001508.3	c.856+102283T>C		intron_variant		ENST00000329321.4	NP_001499.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPR39	ENST00000329321.4	c.856+102283T>C		intron_variant		1	NM_001508.3	ENSP00000327417	P1

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67529 AN: 151928 Hom.: 16507 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.444 AC: 67572 AN: 152046 Hom.: 16521 Cov.: 32 AF XY: 0.441 AC XY: 32793 AN XY: 74292

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.482

Alfa AF: 0.528 Hom.: 9350

Bravo AF: 0.434

Asia WGS AF: 0.363 AC: 1262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs2315598; hg19: chr2-133277754;