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rs7216389

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001165958.2(GSDMB):c.236-1199G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 152,028 control chromosomes in the GnomAD database, including 28,368 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 0.60 ( 28368 hom., cov: 31)

Consequence

GSDMB
NM_001165958.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.23
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GSDMBNM_001165958.2 linkuse as main transcriptc.236-1199G>A intron_variant ENST00000418519.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GSDMBENST00000418519.6 linkuse as main transcriptc.236-1199G>A intron_variant 5 NM_001165958.2 P2Q8TAX9-4

Frequencies

GnomAD3 genomes
AF:
0.597
AC:
90717
AN:
151910
Hom.:
28329
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.788
Gnomad AMI
AF:
0.327
Gnomad AMR
AF:
0.591
Gnomad ASJ
AF:
0.563
Gnomad EAS
AF:
0.729
Gnomad SAS
AF:
0.576
Gnomad FIN
AF:
0.437
Gnomad MID
AF:
0.630
Gnomad NFE
AF:
0.504
Gnomad OTH
AF:
0.597
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.597
AC:
90802
AN:
152028
Hom.:
28368
Cov.:
31
AF XY:
0.595
AC XY:
44237
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.788
Gnomad4 AMR
AF:
0.590
Gnomad4 ASJ
AF:
0.563
Gnomad4 EAS
AF:
0.729
Gnomad4 SAS
AF:
0.576
Gnomad4 FIN
AF:
0.437
Gnomad4 NFE
AF:
0.504
Gnomad4 OTH
AF:
0.599
Alfa
AF:
0.524
Hom.:
46166
Bravo
AF:
0.625
Asia WGS
AF:
0.625
AC:
2176
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
Cadd
Benign
0.012
Dann
Benign
0.66

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7216389; hg19: chr17-38069949; COSMIC: COSV58782744; COSMIC: COSV58782744; API