17-39955101-A-G

Variant names:

• chr17-39955101-A-G
• rs1007654
• ENST00000635792.1:c.-6+1796A>G

Variant summary

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

The ENST00000635792.1(GSDMA):​c.-6+1796A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 152,050 control chromosomes in the GnomAD database, including 36,042 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 0.68 (36042 hom., cov: 32)
• Consequence: GSDMA ENST00000635792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 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+1796A>G		intron_variant	Intron 1 of 11	5		ENSP00000490739.1

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103910 AN: 151932 Hom.: 36012 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.684 AC: 103994 AN: 152050 Hom.: 36042 Cov.: 32 AF XY: 0.687 AC XY: 51063 AN XY: 74308

African (AFR) AF: 0.772 AC: 32037 AN: 41480

American (AMR) AF: 0.697 AC: 10660 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2070 AN: 3466

East Asian (EAS) AF: 0.700 AC: 3614 AN: 5164

South Asian (SAS) AF: 0.687 AC: 3309 AN: 4816

European-Finnish (FIN) AF: 0.686 AC: 7238 AN: 10558

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42967 AN: 67962

Other (OTH) AF: 0.643 AC: 1359 AN: 2112

Alfa AF: 0.651 Hom.: 25791

Bravo AF: 0.691

Asia WGS AF: 0.684 AC: 2379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.71
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1007654; hg19: chr17-38111354;