ENST00000296873.11:c.*1476C>T

Variant names:

• chr5-132757345-G-A
• rs256871
• ENST00000296873.11:c.*1476C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000296873.11(SEPTIN8):​c.*1476C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 985,116 control chromosomes in the GnomAD database, including 12,807 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 0.23 (5311 hom., cov: 32)
  • Exomes 𝑓: 0.12 (7496 hom.)
• Consequence: SEPTIN8 ENST00000296873.11 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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 = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEPTIN8	NM_001098811.2	c.1286+3457C>T		intron_variant	Intron 9 of 9	ENST00000378719.7	NP_001092281.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEPTIN8	ENST00000378719.7	c.1286+3457C>T		intron_variant	Intron 9 of 9	1	NM_001098811.2	ENSP00000367991.2

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34320 AN: 151856 Hom.: 5312 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.197

GnomAD4 exome AF: 0.122 AC: 101996 AN: 833142 Hom.: 7496 Cov.: 31 AF XY: 0.120 AC XY: 46359 AN XY: 384734

African (AFR) AF: 0.344 AC: 5437 AN: 15788

American (AMR) AF: 0.299 AC: 294 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 669 AN: 5152

East Asian (EAS) AF: 0.732 AC: 2656 AN: 3630

South Asian (SAS) AF: 0.132 AC: 2179 AN: 16458

European-Finnish (FIN) AF: 0.283 AC: 81 AN: 286

Middle Eastern (MID) AF: 0.120 AC: 195 AN: 1622

European-Non Finnish (NFE) AF: 0.113 AC: 86059 AN: 761922

Other (OTH) AF: 0.162 AC: 4426 AN: 27300

GnomAD4 genome AF: 0.226 AC: 34360 AN: 151974 Hom.: 5311 Cov.: 32 AF XY: 0.235 AC XY: 17422 AN XY: 74242

African (AFR) AF: 0.334 AC: 13851 AN: 41458

American (AMR) AF: 0.239 AC: 3651 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3472

East Asian (EAS) AF: 0.734 AC: 3783 AN: 5154

South Asian (SAS) AF: 0.165 AC: 793 AN: 4802

European-Finnish (FIN) AF: 0.291 AC: 3065 AN: 10534

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8269 AN: 67958

Other (OTH) AF: 0.200 AC: 422 AN: 2112

Alfa AF: 0.160 Hom.: 4790

Bravo AF: 0.232

Asia WGS AF: 0.401 AC: 1394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.097
DANN	Benign	0.68
PhyloP100		-1.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs256871; hg19: chr5-132093037;