17-39918763-T-C

Position:

• chr17-39918763-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000477054.6(GSDMB):​n.1092A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 133,892 control chromosomes in the GnomAD database, including 20,013 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 0.57 (20013 hom., cov: 26)
  • Exomes 𝑓: 0.58 (4 hom.)
  • Failed GnomAD Quality Control
• Consequence: GSDMB ENST00000477054.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

Genes affected

GSDMB (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.39918763T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSDMB	ENST00000477054.6	n.1092A>G		non_coding_transcript_exon_variant	1/8	5

Frequencies

GnomAD3 genomes AF: 0.575 AC: 76960 AN: 133872 Hom.: 20014 Cov.: 26

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.595

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.583 AC: 21 AN: 36 Hom.: 4 Cov.: 0 AF XY: 0.600 AC XY: 18 AN XY: 30

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.714

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.575 AC: 76965 AN: 133892 Hom.: 20013 Cov.: 26 AF XY: 0.574 AC XY: 37529 AN XY: 65340

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.596

Alfa AF: 0.280 Hom.: 341

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3902920; hg19: chr17-38075016;