16-20046339-G-C

Variant names:

• chr16-20046339-G-C
• rs1902813
• NM_001002911.4:c.128-13670C>G

Variant summary

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

The NM_001002911.4(GPR139):​c.128-13670C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,182 control chromosomes in the GnomAD database, including 3,346 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 0.19 (3346 hom., cov: 33)
• Consequence: GPR139 NM_001002911.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767
• Publications: 2 publications found

Genes affected

GPR139 (HGNC:19995): (G protein-coupled receptor 139) This gene encodes a member of the rhodopsin family of G-protein-coupled receptors. The encoded protein is almost exclusively expressed in the central nervous system. L-tryptophan and L-phenylalanine may act as the physiologic ligands of the encoded protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001002911.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR139	NM_001002911.4	MANE Select	c.128-13670C>G		intron	N/A	NP_001002911.1	Q6DWJ6
	GPR139	NM_001318483.1		c.-152-13670C>G		intron	N/A	NP_001305412.1	Q6DWJ6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR139	ENST00000570682.2	TSL:1 MANE Select	c.128-13670C>G		intron	N/A	ENSP00000458791.2	Q6DWJ6
	GPR139	ENST00000326571.7	TSL:1	n.*74-13670C>G		intron	N/A	ENSP00000370779.5	J3KPI8

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28629 AN: 152064 Hom.: 3347 Cov.: 33

Gnomad AFR AF: 0.0591

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.188 AC: 28632 AN: 152182 Hom.: 3346 Cov.: 33 AF XY: 0.193 AC XY: 14383 AN XY: 74380

African (AFR) AF: 0.0592 AC: 2460 AN: 41538

American (AMR) AF: 0.192 AC: 2942 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3472

East Asian (EAS) AF: 0.371 AC: 1919 AN: 5176

South Asian (SAS) AF: 0.175 AC: 842 AN: 4812

European-Finnish (FIN) AF: 0.327 AC: 3462 AN: 10596

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15655 AN: 67972

Other (OTH) AF: 0.184 AC: 390 AN: 2114

Alfa AF: 0.210 Hom.: 469

Bravo AF: 0.174

Asia WGS AF: 0.214 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.27
DANN	Benign	0.58
PhyloP100		-0.77
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: rs1902813; hg19: chr16-20057661;