rs56298433
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000674.3(ADORA1):c.-212-168G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 152,288 control chromosomes in the GnomAD database, including 33 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: 𝑓 0.012 ( 33 hom., cov: 32)
Consequence
ADORA1
NM_000674.3 intron
NM_000674.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.01
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0122 (1857/152288) while in subpopulation AFR AF= 0.0385 (1600/41562). AF 95% confidence interval is 0.0369. There are 33 homozygotes in gnomad4. There are 940 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1857 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADORA1 | NM_000674.3 | c.-212-168G>T | intron_variant | ENST00000337894.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADORA1 | ENST00000337894.9 | c.-212-168G>T | intron_variant | 2 | NM_000674.3 | P1 | |||
ADORA1 | ENST00000309502.7 | c.-212-168G>T | intron_variant | 1 | P1 | ||||
ADORA1 | ENST00000367236.8 | c.-58+182G>T | intron_variant | 1 | P1 | ||||
ENST00000665660.1 | n.146-65C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0122 AC: 1857AN: 152170Hom.: 33 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0122 AC: 1857AN: 152288Hom.: 33 Cov.: 32 AF XY: 0.0126 AC XY: 940AN XY: 74456
GnomAD4 genome
?
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32
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940
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74456
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72
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at