rs2236418
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000818.3(GAD2):c.-243A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 369,476 control chromosomes in the GnomAD database, including 20,826 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 0.36 ( 14906 hom., cov: 32)
Exomes 𝑓: 0.20 ( 5920 hom. )
Consequence
GAD2
NM_000818.3 5_prime_UTR
NM_000818.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.638
Genes affected
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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=-0.81).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GAD2 | NM_000818.3 | c.-243A>G | 5_prime_UTR_variant | 1/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.355 AC: 53967AN: 151854Hom.: 14858 Cov.: 32
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GnomAD4 exome AF: 0.204 AC: 44455AN: 217504Hom.: 5920 Cov.: 0 AF XY: 0.204 AC XY: 23083AN XY: 113028
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GnomAD4 genome ? AF: 0.356 AC: 54073AN: 151972Hom.: 14906 Cov.: 32 AF XY: 0.353 AC XY: 26224AN XY: 74270
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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