chr17-77281498-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NR_136503.1(SEPTIN9-DT):n.286+114G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00161 in 1,545,440 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0085 ( 22 hom., cov: 33)
Exomes 𝑓: 0.00086 ( 15 hom. )
Consequence
SEPTIN9-DT
NR_136503.1 intron, non_coding_transcript
NR_136503.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.846
Genes affected
SEPTIN9-DT (HGNC:52818): (SEPTIN9 divergent transcript)
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=-0.58).
BP6
?
Variant 17-77281498-C-T is Benign according to our data. Variant chr17-77281498-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1196918.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00852 (1298/152258) while in subpopulation AFR AF= 0.0289 (1199/41556). AF 95% confidence interval is 0.0275. There are 22 homozygotes in gnomad4. There are 628 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 22 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEPTIN9-DT | NR_136503.1 | n.286+114G>A | intron_variant, non_coding_transcript_variant | ||||
SEPTIN9 | NM_001113491.2 | upstream_gene_variant | ENST00000427177.6 | ||||
SEPTIN9 | NM_001293695.2 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEPTIN9-DT | ENST00000701682.1 | n.443+114G>A | intron_variant, non_coding_transcript_variant | ||||||
SEPTIN9 | ENST00000427177.6 | upstream_gene_variant | 1 | NM_001113491.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00852 AC: 1296AN: 152142Hom.: 22 Cov.: 33
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GnomAD3 exomes AF: 0.00189 AC: 269AN: 142550Hom.: 3 AF XY: 0.00135 AC XY: 104AN XY: 77140
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GnomAD4 exome AF: 0.000858 AC: 1195AN: 1393182Hom.: 15 Cov.: 30 AF XY: 0.000730 AC XY: 502AN XY: 687380
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GnomAD4 genome ? AF: 0.00852 AC: 1298AN: 152258Hom.: 22 Cov.: 33 AF XY: 0.00844 AC XY: 628AN XY: 74448
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 07, 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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at