17-39955101-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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 Benign. Variant got -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

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.643

Alfa AF: 0.634 Hom.: 17394

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1007654; hg19: chr17-38111354;