rs369243241
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001788.6(SEPTIN7):c.20C>A(p.Ser7Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000196 in 1,533,796 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S7C) has been classified as Uncertain significance.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
SEPTIN7
NM_001788.6 missense
NM_001788.6 missense
Scores
1
2
15
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.27
Publications
2 publications found
Genes affected
SEPTIN7 (HGNC:1717): (septin 7) This gene encodes a protein that is highly similar to the CDC10 protein of Saccharomyces cerevisiae. The protein also shares similarity with Diff 6 of Drosophila and with H5 of mouse. Each of these similar proteins, including the yeast CDC10, contains a GTP-binding motif. The yeast CDC10 protein is a structural component of the 10 nm filament which lies inside the cytoplasmic membrane and is essential for cytokinesis. This human protein functions in gliomagenesis and in the suppression of glioma cell growth, and it is required for the association of centromere-associated protein E with the kinetochore. Alternative splicing results in multiple transcript variants. Several related pseudogenes have been identified on chromosomes 5, 7, 9, 10, 11, 14, 17 and 19. [provided by RefSeq, Jul 2011]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.23076215).
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SEPTIN7 | ENST00000350320.11 | c.20C>A | p.Ser7Tyr | missense_variant | Exon 1 of 14 | 5 | NM_001788.6 | ENSP00000344868.8 | ||
| SEPTIN7 | ENST00000635175.1 | n.11C>A | non_coding_transcript_exon_variant | Exon 1 of 14 | 2 | ENSP00000489192.1 | ||||
| SEPTIN7 | ENST00000635047.1 | c.-279C>A | 5_prime_UTR_variant | Exon 1 of 7 | 4 | ENSP00000489480.1 |
Frequencies
GnomAD3 genomes 0.00000658 AC: 1AN: 152044Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152044
Hom.:
Cov.:
33
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:
GnomAD4 exome AF: 0.00000145 AC: 2AN: 1381752Hom.: 0 Cov.: 29 AF XY: 0.00000293 AC XY: 2AN XY: 681642 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1381752
Hom.:
Cov.:
29
AF XY:
AC XY:
2
AN XY:
681642
show subpopulations
African (AFR)
AF:
AC:
0
AN:
29702
American (AMR)
AF:
AC:
0
AN:
33404
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24538
East Asian (EAS)
AF:
AC:
1
AN:
32876
South Asian (SAS)
AF:
AC:
0
AN:
77152
European-Finnish (FIN)
AF:
AC:
0
AN:
49104
Middle Eastern (MID)
AF:
AC:
0
AN:
4586
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1073104
Other (OTH)
AF:
AC:
0
AN:
57286
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00000658 AC: 1AN: 152044Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74280 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
152044
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
74280
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41392
American (AMR)
AF:
AC:
0
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3466
East Asian (EAS)
AF:
AC:
0
AN:
5174
South Asian (SAS)
AF:
AC:
0
AN:
4822
European-Finnish (FIN)
AF:
AC:
0
AN:
10608
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67988
Other (OTH)
AF:
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.675
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
DEOGEN2
Benign
T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Benign
.;N;.
REVEL
Benign
Sift
Uncertain
.;D;.
Sift4G
Benign
T;D;D
Polyphen
0.88
.;P;.
Vest4
0.39, 0.58
MutPred
Loss of helix (P = 0.0017);Loss of helix (P = 0.0017);Loss of helix (P = 0.0017);
MVP
0.58
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
gMVP
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
Publications
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