XM_011543241.3:c.*3-8813T>C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XM_011543241.3(S100Z):c.*3-8813T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,770 control chromosomes in the GnomAD database, including 30,789 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 0.63 ( 30789 hom., cov: 30)
Consequence
S100Z
XM_011543241.3 intron
XM_011543241.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.851
Publications
2 publications found
Genes affected
S100Z (HGNC:30367): (S100 calcium binding protein Z) Members of the S100 protein family contain 2 calcium-binding EF-hands and exhibit cell-type specific expression patterns. For additional background information on S100 proteins, see MIM 114085.[supplied by OMIM, Mar 2008]
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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=-0.95).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|
Frequencies
GnomAD3 genomes AF: 0.633 AC: 96022AN: 151652Hom.: 30769 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
96022
AN:
151652
Hom.:
Cov.:
30
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: 0.633 AC: 96083AN: 151770Hom.: 30789 Cov.: 30 AF XY: 0.636 AC XY: 47196AN XY: 74150 show subpopulations
GnomAD4 genome
AF:
AC:
96083
AN:
151770
Hom.:
Cov.:
30
AF XY:
AC XY:
47196
AN XY:
74150
show subpopulations
African (AFR)
AF:
AC:
22791
AN:
41344
American (AMR)
AF:
AC:
10660
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
AC:
2128
AN:
3470
East Asian (EAS)
AF:
AC:
3715
AN:
5164
South Asian (SAS)
AF:
AC:
3688
AN:
4802
European-Finnish (FIN)
AF:
AC:
6395
AN:
10484
Middle Eastern (MID)
AF:
AC:
152
AN:
294
European-Non Finnish (NFE)
AF:
AC:
44664
AN:
67936
Other (OTH)
AF:
AC:
1305
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.508
Heterozygous variant carriers
0
1742
3484
5226
6968
8710
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
788
1576
2364
3152
3940
<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:
2443
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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