1-168085708-C-T

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2

The NM_001375883.1(GPR161):​c.1413G>A​(p.Glu471Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000969 in 1,614,244 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0050 ( 5 hom., cov: 32)
Exomes 𝑓: 0.00055 ( 6 hom. )

Consequence

GPR161
NM_001375883.1 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.11
Variant links:
Genes affected
GPR161 (HGNC:23694): (G protein-coupled receptor 161) The protein encoded by this gene is an orphan G protein-coupled receptor whose ligand is unknown. This gene is overexpressed in triple-negative breast cancer, and disruption of this gene slows the proliferation of basal breast cancer cells. Therefore, this gene is a potential drug target for triple-negative breast cancer. [provided by RefSeq, Mar 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.26).
BP6
Variant 1-168085708-C-T is Benign according to our data. Variant chr1-168085708-C-T is described in ClinVar as [Benign]. Clinvar id is 789948.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=1.12 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00499 (761/152370) while in subpopulation AFR AF= 0.0172 (714/41590). AF 95% confidence interval is 0.0161. There are 5 homozygotes in gnomad4. There are 364 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GPR161NM_001375883.1 linkc.1413G>A p.Glu471Glu synonymous_variant Exon 6 of 6 ENST00000682931.1 NP_001362812.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GPR161ENST00000682931.1 linkc.1413G>A p.Glu471Glu synonymous_variant Exon 6 of 6 NM_001375883.1 ENSP00000506967.1 Q8N6U8-1

Frequencies

GnomAD3 genomes
AF:
0.00496
AC:
755
AN:
152252
Hom.:
5
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0171
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.00209
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000147
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.00140
AC:
352
AN:
251428
Hom.:
1
AF XY:
0.00109
AC XY:
148
AN XY:
135906
show subpopulations
Gnomad AFR exome
AF:
0.0184
Gnomad AMR exome
AF:
0.000896
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000653
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000106
Gnomad OTH exome
AF:
0.00130
GnomAD4 exome
AF:
0.000550
AC:
804
AN:
1461874
Hom.:
6
Cov.:
32
AF XY:
0.000503
AC XY:
366
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.0187
Gnomad4 AMR exome
AF:
0.00103
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000927
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000369
Gnomad4 OTH exome
AF:
0.00109
GnomAD4 genome
AF:
0.00499
AC:
761
AN:
152370
Hom.:
5
Cov.:
32
AF XY:
0.00489
AC XY:
364
AN XY:
74506
show subpopulations
Gnomad4 AFR
AF:
0.0172
Gnomad4 AMR
AF:
0.00209
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000147
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00255
Hom.:
2
Bravo
AF:
0.00564
Asia WGS
AF:
0.00260
AC:
9
AN:
3478
EpiCase
AF:
0.000273
EpiControl
AF:
0.000119

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Jan 23, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.26
CADD
Benign
7.8
DANN
Benign
0.81

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs112752784; hg19: chr1-168054946; API