Genetic Variant ENST00000296873.11:c.*864A>G (chr5-132757957-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000296873.11(SEPTIN8):c.*864A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 985,860 control chromosomes in the GnomAD database, including 29,913 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 ( 16987 hom., cov: 32)

Exomes 𝑓: 0.14 ( 12926 hom. )

Consequence

SEPTIN8
ENST00000296873.11 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.150

Publications

15 publications found

Variant links:

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]

SEPTIN8 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

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 rank	MANE	Protein	UniProt
SEPTIN8	NM_001098811.2 link	c.1286+2845A>G		intron_variant	Intron 9 of 9	ENST00000378719.7	NP_001092281.1	Q92599-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEPTIN8	ENST00000378719.7 link	c.1286+2845A>G		intron_variant	Intron 9 of 9	1	NM_001098811.2	ENSP00000367991.2		Q92599-1

Frequencies

GnomAD3 genomes

AF:

0.364

AC:

55300

AN:

151972

Hom.:

16940

Cov.:

show subpopulations

Gnomad AFR

AF:

0.807

Gnomad AMI

AF:

0.0175

Gnomad AMR

AF:

0.300

Gnomad ASJ

AF:

0.141

Gnomad EAS

AF:

0.735

Gnomad SAS

AF:

0.168

Gnomad FIN

AF:

0.291

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.297

GnomAD4 exome

AF:

0.136

AC:

113239

AN:

833770

Hom.:

12926

Cov.:

AF XY:

0.133

AC XY:

51285

AN XY:

385036

show subpopulations

African (AFR)

AF:

0.857

AC:

13532

AN:

15788

American (AMR)

AF:

0.325

AC:

348

AN:

1072

Ashkenazi Jewish (ASJ)

AF:

0.136

AC:

699

AN:

5154

East Asian (EAS)

AF:

0.733

AC:

2665

AN:

3638

South Asian (SAS)

AF:

0.134

AC:

2208

AN:

16498

European-Finnish (FIN)

AF:

0.275

AC:

AN:

280

Middle Eastern (MID)

AF:

0.167

AC:

271

AN:

1620

European-Non Finnish (NFE)

AF:

0.116

AC:

88288

AN:

762406

Other (OTH)

AF:

0.189

AC:

5151

AN:

27314

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

4765

9531

14296

19062

23827

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.364

AC:

55417

AN:

152090

Hom.:

16987

Cov.:

AF XY:

0.369

AC XY:

27428

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.807

AC:

33450

AN:

41452

American (AMR)

AF:

0.300

AC:

4583

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.141

AC:

488

AN:

3470

East Asian (EAS)

AF:

0.734

AC:

3793

AN:

5170

South Asian (SAS)

AF:

0.168

AC:

809

AN:

4816

European-Finnish (FIN)

AF:

0.291

AC:

3080

AN:

10578

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.125

AC:

8508

AN:

68006

Other (OTH)

AF:

0.301

AC:

634

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1136

2272

3407

4543

5679

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.201

Hom.:

7354

Bravo

AF:

0.392

Asia WGS

AF:

0.431

AC:

1500

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.2

(source)

DANN

Benign

0.48

PhyloP100

0.15

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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ENST00000296873.11:c.*864A>G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over