chr3-98532771-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_005290.4(GPR15):c.738C>T(p.Val246=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00194 in 1,613,908 control chromosomes in the GnomAD database, including 41 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.010 ( 20 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 21 hom. )
Consequence
GPR15
NM_005290.4 synonymous
NM_005290.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.04
Genes affected
GPR15 (HGNC:4469): (G protein-coupled receptor 15) This gene encodes a G protein-coupled receptor that acts as a chemokine receptor for human immunodeficiency virus type 1 and 2. The encoded protein localizes to the cell membrane. [provided by RefSeq, Nov 2012]
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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=-0.7).
BP6
Variant 3-98532771-C-T is Benign according to our data. Variant chr3-98532771-C-T is described in ClinVar as [Benign]. Clinvar id is 791939.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.04 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0104 (1581/152196) while in subpopulation AFR AF= 0.0362 (1501/41506). AF 95% confidence interval is 0.0346. There are 20 homozygotes in gnomad4. There are 734 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 20 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR15 | NM_005290.4 | c.738C>T | p.Val246= | synonymous_variant | 1/1 | ENST00000284311.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR15 | ENST00000284311.5 | c.738C>T | p.Val246= | synonymous_variant | 1/1 | NM_005290.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0103 AC: 1574AN: 152078Hom.: 19 Cov.: 32
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GnomAD3 exomes AF: 0.00280 AC: 704AN: 251326Hom.: 21 AF XY: 0.00203 AC XY: 276AN XY: 135824
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GnomAD4 exome AF: 0.00106 AC: 1549AN: 1461712Hom.: 21 Cov.: 34 AF XY: 0.000917 AC XY: 667AN XY: 727130
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GnomAD4 genome AF: 0.0104 AC: 1581AN: 152196Hom.: 20 Cov.: 32 AF XY: 0.00987 AC XY: 734AN XY: 74402
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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 | Feb 25, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at