rs2315598

Variant names:

• chr2-132520181-T-C
• rs2315598
• NM_001508.3:c.856+102283T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GPR39	NM_001508.3	c.856+102283T>C		intron_variant	Intron 1 of 1	ENST00000329321.4	NP_001499.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR39	ENST00000329321.4	c.856+102283T>C		intron_variant	Intron 1 of 1	1	NM_001508.3	ENSP00000327417.3

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

African (AFR) AF: 0.245 AC: 10181 AN: 41480

American (AMR) AF: 0.504 AC: 7694 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1791 AN: 3470

East Asian (EAS) AF: 0.184 AC: 950 AN: 5168

South Asian (SAS) AF: 0.441 AC: 2119 AN: 4808

European-Finnish (FIN) AF: 0.493 AC: 5209 AN: 10570

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37967 AN: 67954

Other (OTH) AF: 0.482 AC: 1017 AN: 2110

Alfa AF: 0.527 Hom.: 10535

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
PhyloP100		1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2315598; hg19: chr2-133277754;