Genetic Variant GSDMA:c.558+22_558+37delACACACACACACACAC (chr17-39970658-AACACACACACACACAC-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_178171.5(GSDMA):c.558+22_558+37delACACACACACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000831 in 1,203,378 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Exomes 𝑓: 8.3e-7 ( 0 hom. )

Consequence

GSDMA
NM_178171.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.334

Publications

0 publications found

Variant links:

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]

GSDMA links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
GSDMA	NM_178171.5 link	c.558+22_558+37delACACACACACACACAC	intron_variant	Intron 4 of 11	ENST00000301659.9	NP_835465.2
GSDMA	XM_006721832.4 link	c.558+22_558+37delACACACACACACACAC	intron_variant	Intron 4 of 11		XP_006721895.1
GSDMA	XM_017024502.3 link	c.558+22_558+37delACACACACACACACAC	intron_variant	Intron 4 of 10		XP_016879991.1
GSDMA	XM_011524651.4 link	c.132+22_132+37delACACACACACACACAC	intron_variant	Intron 2 of 9		XP_011522953.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
GSDMA	ENST00000301659.9 link	c.558+12_558+27delACACACACACACACAC	intron_variant	Intron 4 of 11	1	NM_178171.5	ENSP00000301659.4
GSDMA	ENST00000635792.1 link	c.558+12_558+27delACACACACACACACAC	intron_variant	Intron 4 of 11	5		ENSP00000490739.1
GSDMA	ENST00000577447.1 link	c.94_109delACACACACACACACAC	downstream_gene_variant		4		ENSP00000461985.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

8.31e-7

AC:

AN:

1203378

Hom.:

AF XY:

0.00000171

AC XY:

AN XY:

586102

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

25690

American (AMR)

AF:

0.00

AC:

AN:

17516

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17716

East Asian (EAS)

AF:

0.00

AC:

AN:

28804

South Asian (SAS)

AF:

0.00

AC:

AN:

56648

European-Finnish (FIN)

AF:

0.00

AC:

AN:

42704

Middle Eastern (MID)

AF:

0.000275

AC:

AN:

3630

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

961520

Other (OTH)

AF:

0.00

AC:

AN:

49150

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over