chr17-77307420-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001113491.2(SEPTIN9):c.76+223G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0689 in 152,294 control chromosomes in the GnomAD database, including 544 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.069 ( 544 hom., cov: 32)
Consequence
SEPTIN9
NM_001113491.2 intron
NM_001113491.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.182
Genes affected
SEPTIN9 (HGNC:7323): (septin 9) This gene is a member of the septin family involved in cytokinesis and cell cycle control. This gene is a candidate for the ovarian tumor suppressor gene. Mutations in this gene cause hereditary neuralgic amyotrophy, also known as neuritis with brachial predilection. A chromosomal translocation involving this gene on chromosome 17 and the MLL gene on chromosome 11 results in acute myelomonocytic leukemia. Multiple alternatively spliced transcript variants encoding different isoforms have been described.[provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 17-77307420-G-A is Benign according to our data. Variant chr17-77307420-G-A is described in ClinVar as [Benign]. Clinvar id is 1296451.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-77307420-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEPTIN9 | NM_001113491.2 | c.76+223G>A | intron_variant | ENST00000427177.6 | |||
SEPTIN9 | NM_001113492.2 | c.-417+223G>A | intron_variant | ||||
SEPTIN9 | NM_001293695.2 | c.19+25866G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEPTIN9 | ENST00000427177.6 | c.76+223G>A | intron_variant | 1 | NM_001113491.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0688 AC: 10477AN: 152176Hom.: 543 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0689 AC: 10499AN: 152294Hom.: 544 Cov.: 32 AF XY: 0.0677 AC XY: 5043AN XY: 74464
GnomAD4 genome
?
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 17, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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