rs7219080

Variant names:

• chr17-39958263-A-C
• rs7219080
• ENST00000635792.1:c.-6+4958A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635792.1(GSDMA):​c.-6+4958A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 151,972 control chromosomes in the GnomAD database, including 32,500 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.65 (32500 hom., cov: 31)
• Consequence: GSDMA ENST00000635792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 19 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSDMA	ENST00000635792.1	c.-6+4958A>C		intron_variant	Intron 1 of 11	5		ENSP00000490739.1

Frequencies

GnomAD3 genomes AF: 0.652 AC: 98983 AN: 151854 Hom.: 32482 Cov.: 31

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.623

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.652 AC: 99048 AN: 151972 Hom.: 32500 Cov.: 31 AF XY: 0.657 AC XY: 48763 AN XY: 74270

African (AFR) AF: 0.664 AC: 27542 AN: 41450

American (AMR) AF: 0.683 AC: 10427 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2010 AN: 3468

East Asian (EAS) AF: 0.698 AC: 3604 AN: 5164

South Asian (SAS) AF: 0.686 AC: 3313 AN: 4830

European-Finnish (FIN) AF: 0.685 AC: 7222 AN: 10546

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42883 AN: 67934

Other (OTH) AF: 0.624 AC: 1315 AN: 2108

Alfa AF: 0.641 Hom.: 18704

Bravo AF: 0.654

Asia WGS AF: 0.667 AC: 2321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	9.1
DANN	Benign	0.54
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs7219080; hg19: chr17-38114516;