1-168085708-C-T
Variant names:
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
NM_001375883.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.11
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]
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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 |
---|---|---|---|---|---|---|---|---|
GPR161 | NM_001375883.1 | c.1413G>A | p.Glu471Glu | synonymous_variant | Exon 6 of 6 | ENST00000682931.1 | NP_001362812.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00496 AC: 755AN: 152252Hom.: 5 Cov.: 32
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GnomAD3 exomes AF: 0.00140 AC: 352AN: 251428Hom.: 1 AF XY: 0.00109 AC XY: 148AN XY: 135906
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GnomAD4 exome AF: 0.000550 AC: 804AN: 1461874Hom.: 6 Cov.: 32 AF XY: 0.000503 AC XY: 366AN XY: 727244
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GnomAD4 genome AF: 0.00499 AC: 761AN: 152370Hom.: 5 Cov.: 32 AF XY: 0.00489 AC XY: 364AN XY: 74506
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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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at