Variant chr17-39970658-AACAC-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_178171.5(GSDMA):c.558+34_558+37del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0155 in 1,347,884 control chromosomes in the GnomAD database, including 1,510 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.071 ( 1179 hom., cov: 0)

Exomes 𝑓: 0.0085 ( 331 hom. )

Consequence

GSDMA
NM_178171.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.334

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 17-39970658-AACAC-A is Benign according to our data. Variant chr17-39970658-AACAC-A is described in ClinVar as [Benign]. Clinvar id is 402913.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
GSDMA	NM_178171.5 linkuse as main transcript	c.558+34_558+37del	intron_variant	ENST00000301659.9
GSDMA	XM_006721832.4 linkuse as main transcript	c.558+34_558+37del	intron_variant
GSDMA	XM_011524651.4 linkuse as main transcript	c.132+34_132+37del	intron_variant
GSDMA	XM_017024502.3 linkuse as main transcript	c.558+34_558+37del	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSDMA	ENST00000301659.9 linkuse as main transcript	c.558+34_558+37del		intron_variant		1	NM_178171.5	P1
GSDMA	ENST00000635792.1 linkuse as main transcript	c.558+34_558+37del		intron_variant		5		P1

Frequencies

GnomAD3 genomes

AF:

0.0704

AC:

10605

AN:

150558

Hom.:

1173

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0435

Gnomad ASJ

AF:

0.00493

Gnomad EAS

AF:

0.000394

Gnomad SAS

AF:

0.00527

Gnomad FIN

AF:

0.000288

Gnomad MID

AF:

0.0710

Gnomad NFE

AF:

0.00339

Gnomad OTH

AF:

0.0692

GnomAD3 exomes

AF:

0.0212

AC:

1097

AN:

51756

Hom.:

AF XY:

0.0165

AC XY:

418

AN XY:

25320

show subpopulations

Gnomad AFR exome

AF:

0.205

Gnomad AMR exome

AF:

0.0255

Gnomad ASJ exome

AF:

0.00675

Gnomad EAS exome

AF:

0.000957

Gnomad SAS exome

AF:

0.00340

Gnomad FIN exome

AF:

0.000635

Gnomad NFE exome

AF:

0.00395

Gnomad OTH exome

AF:

0.0159

GnomAD4 exome

AF:

0.00852

AC:

10205

AN:

1197208

Hom.:

331

AF XY:

0.00791

AC XY:

4614

AN XY:

583130

show subpopulations

Gnomad4 AFR exome

AF:

0.221

Gnomad4 AMR exome

AF:

0.0265

Gnomad4 ASJ exome

AF:

0.00652

Gnomad4 EAS exome

AF:

0.000731

Gnomad4 SAS exome

AF:

0.00349

Gnomad4 FIN exome

AF:

0.000659

Gnomad4 NFE exome

AF:

0.00272

Gnomad4 OTH exome

AF:

0.0209

GnomAD4 genome

AF:

0.0706

AC:

10634

AN:

150676

Hom.:

1179

Cov.:

AF XY:

0.0699

AC XY:

5138

AN XY:

73544

show subpopulations

Gnomad4 AFR

AF:

0.232

Gnomad4 AMR

AF:

0.0434

Gnomad4 ASJ

AF:

0.00493

Gnomad4 EAS

AF:

0.000394

Gnomad4 SAS

AF:

0.00464

Gnomad4 FIN

AF:

0.000288

Gnomad4 NFE

AF:

0.00339

Gnomad4 OTH

AF:

0.0680

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over