Genetic Variant GSDMA:c.558+30_558+37delACACACAC (chr17-39970658-AACACACAC-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.334

Publications

2 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: Benign. The variant received -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	Effect	Exon rank	MANE	Protein
GSDMA	NM_178171.5 link	c.558+30_558+37delACACACAC	intron_variant	Intron 4 of 11	ENST00000301659.9	NP_835465.2
GSDMA	XM_006721832.4 link	c.558+30_558+37delACACACAC	intron_variant	Intron 4 of 11		XP_006721895.1
GSDMA	XM_017024502.3 link	c.558+30_558+37delACACACAC	intron_variant	Intron 4 of 10		XP_016879991.1
GSDMA	XM_011524651.4 link	c.132+30_132+37delACACACAC	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+19delACACACAC	intron_variant	Intron 4 of 11	1	NM_178171.5	ENSP00000301659.4
GSDMA	ENST00000635792.1 link	c.558+12_558+19delACACACAC	intron_variant	Intron 4 of 11	5		ENSP00000490739.1
GSDMA	ENST00000577447.1 link	c.94_101delACACACAC	downstream_gene_variant		4		ENSP00000461985.1

Frequencies

GnomAD3 genomes

AF:

0.386

AC:

58049

AN:

150454

Hom.:

11300

Cov.:

show subpopulations

Gnomad AFR

AF:

0.326

Gnomad AMI

AF:

0.388

Gnomad AMR

AF:

0.379

Gnomad ASJ

AF:

0.386

Gnomad EAS

AF:

0.486

Gnomad SAS

AF:

0.269

Gnomad FIN

AF:

0.390

Gnomad MID

AF:

0.306

Gnomad NFE

AF:

0.424

Gnomad OTH

AF:

0.370

GnomAD2 exomes

AF:

0.391

AC:

20225

AN:

51756

AF XY:

0.386

show subpopulations

Gnomad AFR exome

AF:

0.321

Gnomad AMR exome

AF:

0.377

Gnomad ASJ exome

AF:

0.393

Gnomad EAS exome

AF:

0.486

Gnomad FIN exome

AF:

0.386

Gnomad NFE exome

AF:

0.416

Gnomad OTH exome

AF:

0.387

GnomAD4 exome

AF:

0.400

AC:

465446

AN:

1163390

Hom.:

67553

AF XY:

0.397

AC XY:

224813

AN XY:

566052

show subpopulations

African (AFR)

AF:

0.306

AC:

7779

AN:

25388

American (AMR)

AF:

0.378

AC:

6305

AN:

16680

Ashkenazi Jewish (ASJ)

AF:

0.379

AC:

6378

AN:

16840

East Asian (EAS)

AF:

0.488

AC:

13541

AN:

27766

South Asian (SAS)

AF:

0.285

AC:

15422

AN:

54134

European-Finnish (FIN)

AF:

0.378

AC:

15661

AN:

41478

Middle Eastern (MID)

AF:

0.331

AC:

1104

AN:

3336

European-Non Finnish (NFE)

AF:

0.409

AC:

380337

AN:

930458

Other (OTH)

AF:

0.400

AC:

18919

AN:

47310

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

13291

26582

39872

53163

66454

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13332

26664

39996

53328

66660

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.386

AC:

58089

AN:

150576

Hom.:

11310

Cov.:

AF XY:

0.382

AC XY:

28033

AN XY:

73480

show subpopulations

African (AFR)

AF:

0.326

AC:

13380

AN:

41068

American (AMR)

AF:

0.380

AC:

5765

AN:

15158

Ashkenazi Jewish (ASJ)

AF:

0.386

AC:

1331

AN:

3448

East Asian (EAS)

AF:

0.486

AC:

2462

AN:

5064

South Asian (SAS)

AF:

0.270

AC:

1279

AN:

4736

European-Finnish (FIN)

AF:

0.390

AC:

4055

AN:

10394

Middle Eastern (MID)

AF:

0.300

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.424

AC:

28610

AN:

67442

Other (OTH)

AF:

0.371

AC:

774

AN:

2084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1768

3535

5303

7070

8838

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

558

1116

1674

2232

2790

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.361

Hom.:

981

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.33

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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17-39970658-AACACACACACACACAC-AACACACAC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over