chr1-168085725-A-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001375883.1(GPR161):āc.1396T>Cā(p.Leu466=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00138 in 1,614,254 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.00079 ( 1 hom., cov: 32)
Exomes š: 0.0014 ( 47 hom. )
Consequence
GPR161
NM_001375883.1 synonymous
NM_001375883.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.516
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 -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
Variant 1-168085725-A-G is Benign according to our data. Variant chr1-168085725-A-G is described in ClinVar as [Benign]. Clinvar id is 788083.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.516 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000787 (120/152382) while in subpopulation SAS AF= 0.023 (111/4828). AF 95% confidence interval is 0.0195. There are 1 homozygotes in gnomad4. There are 82 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 47 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR161 | NM_001375883.1 | c.1396T>C | p.Leu466= | synonymous_variant | 6/6 | ENST00000682931.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR161 | ENST00000682931.1 | c.1396T>C | p.Leu466= | synonymous_variant | 6/6 | NM_001375883.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000788 AC: 120AN: 152264Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00285 AC: 717AN: 251412Hom.: 14 AF XY: 0.00369 AC XY: 501AN XY: 135894
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GnomAD4 exome AF: 0.00145 AC: 2114AN: 1461872Hom.: 47 Cov.: 32 AF XY: 0.00200 AC XY: 1455AN XY: 727240
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GnomAD4 genome AF: 0.000787 AC: 120AN: 152382Hom.: 1 Cov.: 32 AF XY: 0.00110 AC XY: 82AN XY: 74512
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 16, 2018 | - - |
Computational scores
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Benign
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DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at