chr8-143559981-G-GAGGGCAGGGCAGGGCAGGGCAGGGC

Position:

• chr8-143559981-G-GAGGGCAGGGCAGGGCAGGGCAGGGC

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_024736.7(GSDMD):​c.410+32_410+33insAGGGCAGGGCAGGGCAGGGCAGGGC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0016 (2 hom., cov: 0)
  • Exomes 𝑓: 0.0019 (10 hom.)
  • Failed GnomAD Quality Control
• Consequence: GSDMD NM_024736.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

Genes affected

GSDMD (HGNC:25697): (gasdermin D) Gasdermin D is a member of the gasdermin family. Members of this family appear to play a role in regulation of epithelial proliferation. Gasdermin D has been suggested to act as a tumor suppressor. Alternatively spliced transcript variants have been described. [provided by RefSeq, Oct 2009]

GSDMD (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GSDMD	NM_024736.7	c.410+32_410+33insAGGGCAGGGCAGGGCAGGGCAGGGC		intron_variant		ENST00000262580.9	NP_079012.3
GSDMD	NM_001166237.1	c.410+32_410+33insAGGGCAGGGCAGGGCAGGGCAGGGC		intron_variant			NP_001159709.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSDMD	ENST00000262580.9	c.410+32_410+33insAGGGCAGGGCAGGGCAGGGCAGGGC		intron_variant		1	NM_024736.7	ENSP00000262580.4

Frequencies

GnomAD3 genomes AF: 0.00159 AC: 241 AN: 152000 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.000677

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.000327

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.0000944

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00259

Gnomad OTH AF: 0.000958

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00185 AC: 2662 AN: 1436472 Hom.: 10 Cov.: 35 AF XY: 0.00178 AC XY: 1274 AN XY: 715454

Gnomad4 AFR exome AF: 0.000305

Gnomad4 AMR exome AF: 0.000344

Gnomad4 ASJ exome AF: 0.000428

Gnomad4 EAS exome AF: 0.0000761

Gnomad4 SAS exome AF: 0.000189

Gnomad4 FIN exome AF: 0.000193

Gnomad4 NFE exome AF: 0.00230

Gnomad4 OTH exome AF: 0.00128

GnomAD4 genome AF: 0.00158 AC: 241 AN: 152118 Hom.: 2 Cov.: 0 AF XY: 0.00155 AC XY: 115 AN XY: 74364

Gnomad4 AFR AF: 0.000675

Gnomad4 AMR AF: 0.000327

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.0000944

Gnomad4 NFE AF: 0.00259

Gnomad4 OTH AF: 0.000948

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs59118283; hg19: chr8-144642151;