rs1001678771

Variant names:

• chr1-168085646-C-G
• rs1001678771
• NM_001375883.1:c.1475G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-168085646-C-G
• chr1-168085646-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001375883.1(GPR161):​c.1475G>C​(p.Arg492Pro) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R492Q) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: GPR161 NM_001375883.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.92

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR161	NM_001375883.1	c.1475G>C	p.Arg492Pro	missense_variant	Exon 6 of 6	ENST00000682931.1	NP_001362812.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR161	ENST00000682931.1	c.1475G>C	p.Arg492Pro	missense_variant	Exon 6 of 6		NM_001375883.1	ENSP00000506967.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Pathogenic	0.17	D
BayesDel_noAF	Uncertain	0.010
CADD	Benign	20
DANN	Uncertain	0.98
DEOGEN2	Benign	0.17	.;.;.;.;T;.;T
Eigen	Benign	0.10
Eigen_PC	Benign	0.0031
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.91	D;D;D;D;.;D;D
M_CAP	Uncertain	0.12	D
MetaRNN	Uncertain	0.55	D;D;D;D;D;D;D
MetaSVM	Uncertain	-0.10	T
MutationAssessor	Benign	1.0	.;.;.;.;L;.;L
PrimateAI	Uncertain	0.65	T
PROVEAN	Benign	-1.5	N;N;.;N;N;N;N
REVEL	Uncertain	0.46
Sift	Uncertain	0.0020	D;D;.;D;D;D;D
Sift4G	Uncertain	0.0080	D;D;D;D;D;D;D
Polyphen		0.95	.;.;.;.;P;.;P
Vest4		0.39
MutPred		0.60		.;.;.;.;Loss of MoRF binding (P = 0.0077);.;Loss of MoRF binding (P = 0.0077);
MVP		0.91
MPC		1.1
ClinPred		0.81	D
GERP RS		3.9
Varity_R		0.42
gMVP		0.53

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

Other links and lift over

dbSNP: rs1001678771; hg19: chr1-168054884;