rs2969180
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_207386.4(SHISA6):c.896-47312G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,960 control chromosomes in the GnomAD database, including 8,987 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 0.34 ( 8987 hom., cov: 32)
Consequence
SHISA6
NM_207386.4 intron
NM_207386.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0480
Genes affected
SHISA6 (HGNC:34491): (shisa family member 6) Predicted to enable ionotropic glutamate receptor binding activity. Predicted to be involved in several processes, including excitatory chemical synaptic transmission; regulation of short-term neuronal synaptic plasticity; and regulation of signal transduction. Predicted to be located in asymmetric, glutamatergic, excitatory synapse. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in glutamatergic synapse; postsynaptic density; and synaptic membrane. Predicted to be integral component of postsynaptic density 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=-0.94).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHISA6 | NM_207386.4 | c.896-47312G>A | intron_variant | ENST00000441885.8 | |||
SHISA6 | NM_001173461.2 | c.800-51156G>A | intron_variant | ||||
SHISA6 | NM_001173462.2 | c.896-51156G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHISA6 | ENST00000441885.8 | c.896-47312G>A | intron_variant | 5 | NM_207386.4 | ||||
SHISA6 | ENST00000409168.7 | c.800-51156G>A | intron_variant | 1 | P1 | ||||
SHISA6 | ENST00000432116.7 | c.896-51156G>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.344 AC: 52255AN: 151842Hom.: 8982 Cov.: 32
GnomAD3 genomes
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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: 0.344 AC: 52278AN: 151960Hom.: 8987 Cov.: 32 AF XY: 0.349 AC XY: 25898AN XY: 74264
GnomAD4 genome
?
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151960
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32
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25898
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74264
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1419
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3478
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