rs9332401
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_007353.3(GNA12):c.525+19828T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,240 control chromosomes in the GnomAD database, including 1,972 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 0.16 ( 1972 hom., cov: 32)
Consequence
GNA12
NM_007353.3 intron
NM_007353.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.412
Genes affected
GNA12 (HGNC:4380): (G protein subunit alpha 12) Predicted to enable D5 dopamine receptor binding activity; G-protein beta/gamma-subunit complex binding activity; and GTPase activity. Involved in regulation of TOR signaling and regulation of proteasomal ubiquitin-dependent protein catabolic process. Located in focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.89).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNA12 | NM_007353.3 | c.525+19828T>C | intron_variant | ENST00000275364.8 | |||
GNA12 | NM_001282441.2 | c.348+19828T>C | intron_variant | ||||
GNA12 | NM_001293092.2 | c.525+19828T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNA12 | ENST00000275364.8 | c.525+19828T>C | intron_variant | 1 | NM_007353.3 | P1 | |||
GNA12 | ENST00000407904.7 | c.348+19828T>C | intron_variant | 2 | |||||
AMZ1 | ENST00000433945.1 | n.333-189A>G | intron_variant, non_coding_transcript_variant | 4 | |||||
GNA12 | ENST00000471281.5 | n.426+19620T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.157 AC: 23820AN: 152122Hom.: 1968 Cov.: 32
GnomAD3 genomes
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23820
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152122
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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: 0.157 AC: 23835AN: 152240Hom.: 1972 Cov.: 32 AF XY: 0.153 AC XY: 11399AN XY: 74454
GnomAD4 genome
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23835
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32
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11399
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74454
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709
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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