rs7216389
Variant names:
Variant summary
Our verdict is Benign. The variant received -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
NM_001165958.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.23
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 was made for transcript
Our verdict: Benign. The variant received -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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.597 AC: 90717AN: 151910Hom.: 28329 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
90717
AN:
151910
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.597 AC: 90802AN: 152028Hom.: 28368 Cov.: 31 AF XY: 0.595 AC XY: 44237AN XY: 74290 show subpopulations
GnomAD4 genome
AF:
AC:
90802
AN:
152028
Hom.:
Cov.:
31
AF XY:
AC XY:
44237
AN XY:
74290
Gnomad4 AFR
AF:
AC:
0.788239
AN:
0.788239
Gnomad4 AMR
AF:
AC:
0.590421
AN:
0.590421
Gnomad4 ASJ
AF:
AC:
0.563185
AN:
0.563185
Gnomad4 EAS
AF:
AC:
0.729207
AN:
0.729207
Gnomad4 SAS
AF:
AC:
0.575997
AN:
0.575997
Gnomad4 FIN
AF:
AC:
0.43737
AN:
0.43737
Gnomad4 NFE
AF:
AC:
0.503723
AN:
0.503723
Gnomad4 OTH
AF:
AC:
0.599146
AN:
0.599146
Heterozygous variant carriers
0
1796
3592
5388
7184
8980
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
744
1488
2232
2976
3720
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2176
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism (auto)
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at