rs16837705

Variant names:

• chr2-132596254-A-G
• rs16837705
• NM_001508.3:c.857-48847A>G

Variant summary

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

The NM_001508.3(GPR39):​c.857-48847A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 151,976 control chromosomes in the GnomAD database, including 3,942 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 0.22 (3942 hom., cov: 32)
• Consequence: GPR39 NM_001508.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470
• Publications: 7 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001508.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR39	NM_001508.3	MANE Select	c.857-48847A>G		intron	N/A	NP_001499.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR39	ENST00000329321.4	TSL:1 MANE Select	c.857-48847A>G		intron	N/A	ENSP00000327417.3

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33446 AN: 151858 Hom.: 3933 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.220 AC: 33487 AN: 151976 Hom.: 3942 Cov.: 32 AF XY: 0.221 AC XY: 16384 AN XY: 74270

African (AFR) AF: 0.286 AC: 11862 AN: 41462

American (AMR) AF: 0.244 AC: 3731 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 577 AN: 3464

East Asian (EAS) AF: 0.116 AC: 601 AN: 5162

South Asian (SAS) AF: 0.193 AC: 928 AN: 4796

European-Finnish (FIN) AF: 0.187 AC: 1975 AN: 10554

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13223 AN: 67946

Other (OTH) AF: 0.215 AC: 452 AN: 2106

Alfa AF: 0.202 Hom.: 10327

Bravo AF: 0.225

Asia WGS AF: 0.172 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.5
DANN	Benign	0.51
PhyloP100		0.47
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: rs16837705; hg19: chr2-133353827;