rs1080708
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001400265.1(SOGA3):c.1486-6236A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,926 control chromosomes in the GnomAD database, including 32,989 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 0.66 ( 32989 hom., cov: 31)
Consequence
SOGA3
NM_001400265.1 intron
NM_001400265.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.970
Genes affected
SOGA3 (HGNC:21494): (MTCL family member 3) Predicted to be involved in regulation of autophagy. Predicted to be located in extracellular space. Predicted to be integral component of membrane. [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=-0.99).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOGA3 | NM_001400265.1 | c.1486-6236A>C | intron_variant | ENST00000525778.6 | |||
SOGA3-KIAA0408 | NR_174482.1 | n.2331-6236A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOGA3 | ENST00000525778.6 | c.1486-6236A>C | intron_variant | 5 | NM_001400265.1 | P2 | |||
SOGA3 | ENST00000465909.3 | c.1486-6236A>C | intron_variant | 5 | A2 | ||||
SOGA3 | ENST00000703793.1 | c.939-6236A>C | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.657 AC: 99684AN: 151808Hom.: 32947 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.657 AC: 99786AN: 151926Hom.: 32989 Cov.: 31 AF XY: 0.653 AC XY: 48472AN XY: 74248
GnomAD4 genome
?
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99786
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31
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48472
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74248
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2142
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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