17-39970658-AACACACACACACAC-AACACAC
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_178171.5(GSDMA):c.558+30_558+37delACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 1,313,966 control chromosomes in the GnomAD database, including 78,863 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.39 ( 11310 hom., cov: 0)
Exomes 𝑓: 0.40 ( 67553 hom. )
Consequence
GSDMA
NM_178171.5 intron
NM_178171.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.334
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 Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GSDMA | NM_178171.5 | c.558+30_558+37delACACACAC | intron_variant | ENST00000301659.9 | NP_835465.2 | |||
GSDMA | XM_006721832.4 | c.558+30_558+37delACACACAC | intron_variant | XP_006721895.1 | ||||
GSDMA | XM_017024502.3 | c.558+30_558+37delACACACAC | intron_variant | XP_016879991.1 | ||||
GSDMA | XM_011524651.4 | c.132+30_132+37delACACACAC | intron_variant | XP_011522953.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GSDMA | ENST00000301659.9 | c.558+12_558+19delACACACAC | intron_variant | 1 | NM_178171.5 | ENSP00000301659.4 | ||||
GSDMA | ENST00000635792.1 | c.558+12_558+19delACACACAC | intron_variant | 5 | ENSP00000490739.1 |
Frequencies
GnomAD3 genomes AF: 0.386 AC: 58049AN: 150454Hom.: 11300 Cov.: 0
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GnomAD3 exomes AF: 0.391 AC: 20225AN: 51756Hom.: 2972 AF XY: 0.386 AC XY: 9766AN XY: 25320
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GnomAD4 exome AF: 0.400 AC: 465446AN: 1163390Hom.: 67553 AF XY: 0.397 AC XY: 224813AN XY: 566052
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GnomAD4 genome AF: 0.386 AC: 58089AN: 150576Hom.: 11310 Cov.: 0 AF XY: 0.382 AC XY: 28033AN XY: 73480
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at