NM_001002911.4:c.128-16839G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001002911.4(GPR139):​c.128-16839G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,188 control chromosomes in the GnomAD database, including 2,994 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 0.18 ( 2994 hom., cov: 33)

Consequence

GPR139
NM_001002911.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.279

Publications

3 publications found
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GPR139NM_001002911.4 linkc.128-16839G>A intron_variant Intron 1 of 1 ENST00000570682.2 NP_001002911.1 Q6DWJ6A0A142CHG1
GPR139NM_001318483.1 linkc.-152-16839G>A intron_variant Intron 2 of 2 NP_001305412.1 Q6DWJ6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GPR139ENST00000570682.2 linkc.128-16839G>A intron_variant Intron 1 of 1 1 NM_001002911.4 ENSP00000458791.2 Q6DWJ6
GPR139ENST00000326571.7 linkn.*74-16839G>A intron_variant Intron 2 of 2 1 ENSP00000370779.5 J3KPI8

Frequencies

GnomAD3 genomes
AF:
0.177
AC:
26888
AN:
152070
Hom.:
2996
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0541
Gnomad AMI
AF:
0.329
Gnomad AMR
AF:
0.187
Gnomad ASJ
AF:
0.161
Gnomad EAS
AF:
0.376
Gnomad SAS
AF:
0.170
Gnomad FIN
AF:
0.308
Gnomad MID
AF:
0.158
Gnomad NFE
AF:
0.213
Gnomad OTH
AF:
0.174
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.177
AC:
26881
AN:
152188
Hom.:
2994
Cov.:
33
AF XY:
0.182
AC XY:
13538
AN XY:
74390
show subpopulations
African (AFR)
AF:
0.0539
AC:
2239
AN:
41522
American (AMR)
AF:
0.187
AC:
2864
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
0.161
AC:
558
AN:
3472
East Asian (EAS)
AF:
0.376
AC:
1943
AN:
5172
South Asian (SAS)
AF:
0.170
AC:
819
AN:
4814
European-Finnish (FIN)
AF:
0.308
AC:
3258
AN:
10570
Middle Eastern (MID)
AF:
0.146
AC:
43
AN:
294
European-Non Finnish (NFE)
AF:
0.213
AC:
14494
AN:
68022
Other (OTH)
AF:
0.172
AC:
363
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1124
2248
3372
4496
5620
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
296
592
888
1184
1480
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.192
Hom.:
8912
Bravo
AF:
0.165
Asia WGS
AF:
0.213
AC:
738
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
5.3
DANN
Benign
0.74
PhyloP100
0.28
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

Publications

Other links and lift over

dbSNP: rs12931939; hg19: chr16-20060830; API