chr17-39970658-A-AAC
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_178171.5(GSDMA):c.558+36_558+37dup variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0040 ( 2 hom., cov: 0)
Exomes 𝑓: 0.0060 ( 2 hom. )
Consequence
GSDMA
NM_178171.5 intron
NM_178171.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.827
Genes affected
GSDMA (HGNC:13311): (gasdermin A) Predicted to enable phosphatidylinositol-4,5-bisphosphate binding activity; phosphatidylinositol-4-phosphate binding activity; and phosphatidylserine binding activity. Involved in apoptotic process. Located in perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSDMA | NM_178171.5 | c.558+36_558+37dup | intron_variant | ENST00000301659.9 | |||
GSDMA | XM_006721832.4 | c.558+36_558+37dup | intron_variant | ||||
GSDMA | XM_011524651.4 | c.132+36_132+37dup | intron_variant | ||||
GSDMA | XM_017024502.3 | c.558+36_558+37dup | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSDMA | ENST00000301659.9 | c.558+36_558+37dup | intron_variant | 1 | NM_178171.5 | P1 | |||
GSDMA | ENST00000635792.1 | c.558+36_558+37dup | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00396 AC: 596AN: 150608Hom.: 2 Cov.: 0
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GnomAD3 exomes AF: 0.00305 AC: 158AN: 51756Hom.: 0 AF XY: 0.00284 AC XY: 72AN XY: 25320
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GnomAD4 exome AF: 0.00596 AC: 7159AN: 1201914Hom.: 2 Cov.: 0 AF XY: 0.00578 AC XY: 3383AN XY: 585382
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GnomAD4 genome AF: 0.00395 AC: 596AN: 150730Hom.: 2 Cov.: 0 AF XY: 0.00352 AC XY: 259AN XY: 73562
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ClinVar
Not reported inComputational scores
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at