rs758377
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001368771.2(SEPTIN4):c.1615-2785A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.841 in 151,548 control chromosomes in the GnomAD database, including 53,813 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.84 ( 53794 hom., cov: 29)
Exomes 𝑓: 0.77 ( 19 hom. )
Consequence
SEPTIN4
NM_001368771.2 intron
NM_001368771.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.69
Genes affected
SEPTIN4 (HGNC:9165): (septin 4) This gene is a member of the septin family of nucleotide binding proteins, originally described in yeast as cell division cycle regulatory proteins. Septins are highly conserved in yeast, Drosophila, and mouse, and appear to regulate cytoskeletal organization. Disruption of septin function disturbs cytokinesis and results in large multinucleate or polyploid cells. This gene is highly expressed in brain and heart. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. One of the isoforms (known as ARTS) is distinct; it is localized to the mitochondria, and has a role in apoptosis and cancer. [provided by RefSeq, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEPTIN4 | NM_001368771.2 | c.1615-2785A>G | intron_variant | ENST00000672673.2 | |||
SEPTIN4-AS1 | NR_110810.1 | n.258+3946T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEPTIN4 | ENST00000672673.2 | c.1615-2785A>G | intron_variant | NM_001368771.2 | P1 | ||||
SEPTIN4-AS1 | ENST00000580589.5 | n.258+3946T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.841 AC: 127249AN: 151374Hom.: 53730 Cov.: 29
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GnomAD4 exome AF: 0.767 AC: 46AN: 60Hom.: 19 AF XY: 0.737 AC XY: 28AN XY: 38
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GnomAD4 genome ? AF: 0.841 AC: 127372AN: 151488Hom.: 53794 Cov.: 29 AF XY: 0.844 AC XY: 62411AN XY: 73930
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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