rs3902920

Variant names:

• chr17-39918763-T-A
• rs3902920
• ENST00000901434.1:c.-1447A>T

Your query was ambiguous. Multiple possible variants found:

• chr17-39918763-T-A
• chr17-39918763-T-C
• chr17-39918763-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000901434.1(GSDMB):​c.-1447A>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000746 in 134,008 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000075 (0 hom., cov: 26)
• Consequence: GSDMB ENST00000901434.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 10 publications found

Genes affected

GSDMB (HGNC:23690): (gasdermin B) This gene encodes a member of the gasdermin-domain containing protein family. Other gasdermin-family genes are implicated in the regulation of apoptosis in epithelial cells, and are linked to cancer. Alternative splicing and the use of alternative promoters results in multiple transcript variants. Additional variants have been described, but they are candidates for nonsense-mediated mRNA decay (NMD) and are unlikely to be protein-coding. [provided by RefSeq, Nov 2016]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000901434.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSDMB	NM_001165958.2	MANE Select	c.-244A>T		upstream_gene	N/A	NP_001159430.1	Q8TAX9-4
	GSDMB	NM_001388420.1		c.-1447A>T		upstream_gene	N/A	NP_001375349.1	Q8TAX9-4
	GSDMB	NM_001165959.2		c.-235A>T		upstream_gene	N/A	NP_001159431.1	Q8TAX9-6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSDMB	ENST00000901434.1		c.-1447A>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 9	ENSP00000571493.1
	GSDMB	ENST00000901434.1		c.-1447A>T		5_prime_UTR	Exon 1 of 9	ENSP00000571493.1
	GSDMB	ENST00000477054.6	TSL:5	n.1092A>T		non_coding_transcript_exon	Exon 1 of 8

Frequencies

GnomAD3 genomes AF: 0.00000746 AC: 1 AN: 134008 Hom.: 0 Cov.: 26

Gnomad AFR AF: 0.0000304

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.00000746 AC: 1 AN: 134008 Hom.: 0 Cov.: 26 AF XY: 0.0000153 AC XY: 1 AN XY: 65382

African (AFR) AF: 0.0000304 AC: 1 AN: 32862

American (AMR) AF: 0.00 AC: 0 AN: 14004

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3204

East Asian (EAS) AF: 0.00 AC: 0 AN: 5032

South Asian (SAS) AF: 0.00 AC: 0 AN: 4512

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8738

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 280

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 62776

Other (OTH) AF: 0.00 AC: 0 AN: 1818

Alfa AF: 0.00 Hom.: 3263

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.26
PhyloP100		-0.36
PromoterAI		-0.024	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3902920; hg19: chr17-38075016;