rs12805507
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000528582.5(GAS2):c.-21+9505C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,168 control chromosomes in the GnomAD database, including 2,101 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 0.15 ( 2101 hom., cov: 32)
Consequence
GAS2
ENST00000528582.5 intron
ENST00000528582.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.285
Genes affected
GAS2 (HGNC:4167): (growth arrest specific 2) The protein encoded by this gene is a caspase-3 substrate that plays a role in regulating microfilament and cell shape changes during apoptosis. It can also modulate cell susceptibility to p53-dependent apoptosis by inhibiting calpain activity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2017]
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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=-0.73).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GAS2 | XM_011519972.4 | c.-21+6925C>T | intron_variant | ||||
GAS2 | XM_047426745.1 | c.-6052+6925C>T | intron_variant | ||||
GAS2 | XM_047426746.1 | c.-21+6925C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GAS2 | ENST00000528582.5 | c.-21+9505C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.150 AC: 22815AN: 152050Hom.: 2100 Cov.: 32
GnomAD3 genomes
?
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22815
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152050
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.150 AC: 22822AN: 152168Hom.: 2101 Cov.: 32 AF XY: 0.153 AC XY: 11350AN XY: 74402
GnomAD4 genome
?
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22822
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152168
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32
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11350
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74402
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Asia WGS
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491
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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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at