X-119663525-C-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_145799.4(SEPTIN6):​c.298G>A​(p.Val100Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000617 in 1,021,501 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 14 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00023 ( 0 hom., 4 hem., cov: 21)
Exomes 𝑓: 0.000042 ( 0 hom. 10 hem. )

Consequence

SEPTIN6
NM_145799.4 missense

Scores

1
6
10

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.56
Variant links:
Genes affected
SEPTIN6 (HGNC:15848): (septin 6) This gene is a member of the septin family of GTPases. Members of this family are required for cytokinesis. One version of pediatric acute myeloid leukemia is the result of a reciprocal translocation between chromosomes 11 and X, with the breakpoint associated with the genes encoding the mixed-lineage leukemia and septin 2 proteins. This gene encodes four transcript variants encoding three distinct isoforms. An additional transcript variant has been identified, but its biological validity has not been determined. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.12011221).
BS2
High Hemizygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SEPTIN6NM_145799.4 linkc.298G>A p.Val100Ile missense_variant Exon 3 of 11 ENST00000394610.7 NP_665798.1 Q14141-2Q541S4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SEPTIN6ENST00000394610.7 linkc.298G>A p.Val100Ile missense_variant Exon 3 of 11 1 NM_145799.4 ENSP00000378108.1 Q14141-2

Frequencies

GnomAD3 genomes
AF:
0.000235
AC:
24
AN:
102181
Hom.:
0
Cov.:
21
AF XY:
0.000140
AC XY:
4
AN XY:
28473
show subpopulations
Gnomad AFR
AF:
0.000667
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000426
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:
0.000714
GnomAD3 exomes
AF:
0.0000672
AC:
12
AN:
178659
Hom.:
0
AF XY:
0.0000157
AC XY:
1
AN XY:
63685
show subpopulations
Gnomad AFR exome
AF:
0.000617
Gnomad AMR exome
AF:
0.0000383
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000746
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000248
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000424
AC:
39
AN:
919257
Hom.:
0
Cov.:
32
AF XY:
0.0000331
AC XY:
10
AN XY:
301837
show subpopulations
Gnomad4 AFR exome
AF:
0.000334
Gnomad4 AMR exome
AF:
0.000136
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000736
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000357
Gnomad4 OTH exome
AF:
0.0000295
GnomAD4 genome
AF:
0.000235
AC:
24
AN:
102244
Hom.:
0
Cov.:
21
AF XY:
0.000140
AC XY:
4
AN XY:
28520
show subpopulations
Gnomad4 AFR
AF:
0.000666
Gnomad4 AMR
AF:
0.000425
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000705
Alfa
AF:
0.000142
Hom.:
0
Bravo
AF:
0.000344
ESP6500AA
AF:
0.000782
AC:
3
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000412
AC:
5

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Aug 05, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.298G>A (p.V100I) alteration is located in exon 3 (coding exon 3) of the SEPT6 gene. This alteration results from a G to A substitution at nucleotide position 298, causing the valine (V) at amino acid position 100 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.33
T
BayesDel_noAF
Benign
-0.40
CADD
Benign
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.043
.;.;.;T;.;T
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Uncertain
0.96
.;D;.;D;D;D
M_CAP
Uncertain
0.28
D
MetaRNN
Benign
0.12
T;T;T;T;T;T
MetaSVM
Uncertain
-0.24
T
MutationAssessor
Benign
1.7
L;L;L;.;L;L
PrimateAI
Uncertain
0.65
T
PROVEAN
Benign
-0.83
N;N;N;N;N;N
REVEL
Benign
0.16
Sift
Uncertain
0.019
D;D;D;D;D;D
Sift4G
Benign
0.15
T;T;T;T;T;T
Polyphen
0.0080
.;.;.;.;.;B
Vest4
0.51
MVP
0.31
MPC
0.53
ClinPred
0.088
T
GERP RS
4.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.44
gMVP
0.39

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: rs138699101; hg19: chrX-118797488; API