17-39970658-AACACACACACACAC-AACACACACACAC

Position:

• chr17-39970658-AACACACACACACAC-AACACACACACAC

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_178171.5(GSDMA):​c.558+36_558+37del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00666 in 1,340,454 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0017 (1 hom., cov: 0)
  • Exomes 𝑓: 0.0073 (1 hom.)
• Consequence: GSDMA NM_178171.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GSDMA	NM_178171.5	c.558+36_558+37del		intron_variant		ENST00000301659.9
GSDMA	XM_006721832.4	c.558+36_558+37del		intron_variant
GSDMA	XM_011524651.4	c.132+36_132+37del		intron_variant
GSDMA	XM_017024502.3	c.558+36_558+37del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSDMA	ENST00000301659.9	c.558+36_558+37del		intron_variant		1	NM_178171.5	P1
GSDMA	ENST00000635792.1	c.558+36_558+37del		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.00171 AC: 257 AN: 150576 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00166

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000330

Gnomad ASJ AF: 0.000870

Gnomad EAS AF: 0.000197

Gnomad SAS AF: 0.00126

Gnomad FIN AF: 0.000385

Gnomad MID AF: 0.00323

Gnomad NFE AF: 0.00244

Gnomad OTH AF: 0.00194

GnomAD3 exomes AF: 0.0113 AC: 587 AN: 51756 Hom.: 0 AF XY: 0.0118 AC XY: 298 AN XY: 25320

Gnomad AFR exome AF: 0.0128

Gnomad AMR exome AF: 0.00385

Gnomad ASJ exome AF: 0.00787

Gnomad EAS exome AF: 0.00446

Gnomad SAS exome AF: 0.0132

Gnomad FIN exome AF: 0.0187

Gnomad NFE exome AF: 0.0109

Gnomad OTH exome AF: 0.0113

GnomAD4 exome AF: 0.00729 AC: 8669 AN: 1189756 Hom.: 1 AF XY: 0.00741 AC XY: 4293 AN XY: 579402

Gnomad4 AFR exome AF: 0.00847

Gnomad4 AMR exome AF: 0.00436

Gnomad4 ASJ exome AF: 0.00685

Gnomad4 EAS exome AF: 0.00298

Gnomad4 SAS exome AF: 0.0103

Gnomad4 FIN exome AF: 0.0133

Gnomad4 NFE exome AF: 0.00707

Gnomad4 OTH exome AF: 0.00632

GnomAD4 genome AF: 0.00170 AC: 256 AN: 150698 Hom.: 1 Cov.: 0 AF XY: 0.00159 AC XY: 117 AN XY: 73554

Gnomad4 AFR AF: 0.00165

Gnomad4 AMR AF: 0.000329

Gnomad4 ASJ AF: 0.000870

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00126

Gnomad4 FIN AF: 0.000385

Gnomad4 NFE AF: 0.00244

Gnomad4 OTH AF: 0.00192

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs58338887; hg19: chr17-38126911;