1-203129147-T-G
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_000674.3(ADORA1):āc.306T>Gā(p.Ala102=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 1,613,614 control chromosomes in the GnomAD database, including 84,762 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.26 ( 6012 hom., cov: 32)
Exomes š: 0.32 ( 78750 hom. )
Consequence
ADORA1
NM_000674.3 synonymous
NM_000674.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.95
Genes affected
ADORA1 (HGNC:262): (adenosine A1 receptor) The protein encoded by this gene is an adenosine receptor that belongs to the G-protein coupled receptor 1 family. There are 3 types of adenosine receptors, each with a specific pattern of ligand binding and tissue distribution, and together they regulate a diverse set of physiologic functions. The type A1 receptors inhibit adenylyl cyclase, and play a role in the fertilization process. Animal studies also suggest a role for A1 receptors in kidney function and ethanol intoxication. Transcript variants with alternative splicing in the 5' UTR have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP7
Synonymous conserved (PhyloP=-3.95 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADORA1 | NM_000674.3 | c.306T>G | p.Ala102= | synonymous_variant | 3/4 | ENST00000337894.9 | NP_000665.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADORA1 | ENST00000337894.9 | c.306T>G | p.Ala102= | synonymous_variant | 3/4 | 2 | NM_000674.3 | ENSP00000338435 | P1 | |
ADORA1 | ENST00000309502.7 | c.306T>G | p.Ala102= | synonymous_variant | 5/6 | 1 | ENSP00000308549 | P1 | ||
ADORA1 | ENST00000367236.8 | c.306T>G | p.Ala102= | synonymous_variant | 2/3 | 1 | ENSP00000356205 | P1 | ||
ADORA1 | ENST00000367235.1 | c.306T>G | p.Ala102= | synonymous_variant | 2/3 | 2 | ENSP00000356204 |
Frequencies
GnomAD3 genomes AF: 0.262 AC: 39814AN: 152018Hom.: 6008 Cov.: 32
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GnomAD3 exomes AF: 0.306 AC: 76837AN: 250778Hom.: 12676 AF XY: 0.317 AC XY: 43013AN XY: 135490
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GnomAD4 exome AF: 0.323 AC: 472360AN: 1461478Hom.: 78750 Cov.: 49 AF XY: 0.327 AC XY: 237740AN XY: 727006
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GnomAD4 genome AF: 0.262 AC: 39831AN: 152136Hom.: 6012 Cov.: 32 AF XY: 0.263 AC XY: 19535AN XY: 74380
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Not reported inComputational 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