rs30533

chr5-132759282-G-Achr5-132759282-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001098811.2(SEPTIN8):c.1286+1520C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,970 control chromosomes in the GnomAD database, including 16,953 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 0.36 (16953 hom., cov: 32)
• Consequence: SEPTIN8 NM_001098811.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

SEPTIN8 (HGNC:16511): (septin 8) 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. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEPTIN8	NM_001098811.2	c.1286+1520C>T		intron_variant		ENST00000378719.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEPTIN8	ENST00000378719.7	c.1286+1520C>T		intron_variant		1	NM_001098811.2	P3

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55217 AN: 151852 Hom.: 16906 Cov.: 32

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.297

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.364 AC: 55334 AN: 151970 Hom.: 16953 Cov.: 32 AF XY: 0.369 AC XY: 27384 AN XY: 74290

Gnomad4 AFR AF: 0.807

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.301

Alfa AF: 0.263 Hom.: 1228

Bravo AF: 0.392

Asia WGS AF: 0.430 AC: 1498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	0.76
Dann	Benign	0.63

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

Other links and lift over

dbSNP: rs30533; hg19: chr5-132094974;