chr7-55843057-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_207366.3(SEPTIN14):c.443G>A(p.Arg148His) variant causes a missense change. The variant allele was found at a frequency of 0.0000417 in 1,607,988 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00022 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
SEPTIN14
NM_207366.3 missense
NM_207366.3 missense
Scores
4
10
5
Clinical Significance
Conservation
PhyloP100: 6.59
Genes affected
SEPTIN14 (HGNC:33280): (septin 14) SEPT14 is a member of the highly conserved septin family of GTP-binding cytoskeletal proteins implicated in membrane transport, apoptosis, cell polarity, cell cycle regulation, cytokinesis, and other cellular functions (Peterson et al., 2007 [PubMed 17922164]).[supplied by OMIM, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEPTIN14 | NM_207366.3 | c.443G>A | p.Arg148His | missense_variant | 5/10 | ENST00000388975.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEPTIN14 | ENST00000388975.4 | c.443G>A | p.Arg148His | missense_variant | 5/10 | 2 | NM_207366.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152088Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000621 AC: 15AN: 241404Hom.: 0 AF XY: 0.0000459 AC XY: 6AN XY: 130848
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GnomAD4 exome AF: 0.0000234 AC: 34AN: 1455782Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 723742
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GnomAD4 genome AF: 0.000217 AC: 33AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74410
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2023 | The c.443G>A (p.R148H) alteration is located in exon 5 (coding exon 4) of the SEPT14 gene. This alteration results from a G to A substitution at nucleotide position 443, causing the arginine (R) at amino acid position 148 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Pathogenic
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Uncertain
D
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
H
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at