Genetic Variant SEPTIN12:p.Val158Val (chr16-4783969-C-T) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_144605.5(SEPTIN12):c.474G>A(p.Val158Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 1,613,832 control chromosomes in the GnomAD database, including 62,103 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 5019 hom., cov: 32)

Exomes 𝑓: 0.27 ( 57084 hom. )

Consequence

SEPTIN12
NM_144605.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2O:1

Conservation

PhyloP100: 0.0850

Variant links:

Genes affected

SEPTIN12 (HGNC:26348): (septin 12) This gene encodes a guanine-nucleotide binding protein and member of the septin family of cytoskeletal GTPases. Septins play important roles in cytokinesis, exocytosis, embryonic development, and membrane dynamics. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

SEPTIN12 links:

ENSG00000285952 (HGNC:):

ENSG00000285952 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 16-4783969-C-T is Benign according to our data. Variant chr16-4783969-C-T is described in ClinVar as [Benign]. Clinvar id is 37113.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEPTIN12	NM_144605.5 link	c.474G>A	p.Val158Val	synonymous_variant	Exon 5 of 10	ENST00000268231.13	NP_653206.2	Q8IYM1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEPTIN12	ENST00000268231.13 link	c.474G>A	p.Val158Val	synonymous_variant	Exon 5 of 10	1	NM_144605.5	ENSP00000268231.8		Q8IYM1-1

Frequencies

GnomAD3 genomes

AF:

0.250

AC:

38077

AN:

152036

Hom.:

4997

Cov.:

show subpopulations

Gnomad AFR

AF:

0.198

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.280

Gnomad ASJ

AF:

0.342

Gnomad EAS

AF:

0.317

Gnomad SAS

AF:

0.413

Gnomad FIN

AF:

0.171

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.267

Gnomad OTH

AF:

0.272

GnomAD3 exomes

AF:

0.290

AC:

72791

AN:

251296

Hom.:

11262

AF XY:

0.294

AC XY:

39911

AN XY:

135856

show subpopulations

Gnomad AFR exome

AF:

0.194

Gnomad AMR exome

AF:

0.338

Gnomad ASJ exome

AF:

0.348

Gnomad EAS exome

AF:

0.305

Gnomad SAS exome

AF:

0.414

Gnomad FIN exome

AF:

0.184

Gnomad NFE exome

AF:

0.268

Gnomad OTH exome

AF:

0.282

GnomAD4 exome

AF:

0.275

AC:

401912

AN:

1461678

Hom.:

57084

Cov.:

AF XY:

0.279

AC XY:

202872

AN XY:

727160

show subpopulations

Gnomad4 AFR exome

AF:

0.193

Gnomad4 AMR exome

AF:

0.330

Gnomad4 ASJ exome

AF:

0.344

Gnomad4 EAS exome

AF:

0.327

Gnomad4 SAS exome

AF:

0.405

Gnomad4 FIN exome

AF:

0.193

Gnomad4 NFE exome

AF:

0.265

Gnomad4 OTH exome

AF:

0.287

GnomAD4 genome

AF:

0.251

AC:

38140

AN:

152154

Hom.:

5019

Cov.:

AF XY:

0.250

AC XY:

18605

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.199

Gnomad4 AMR

AF:

0.281

Gnomad4 ASJ

AF:

0.342

Gnomad4 EAS

AF:

0.317

Gnomad4 SAS

AF:

0.412

Gnomad4 FIN

AF:

0.171

Gnomad4 NFE

AF:

0.267

Gnomad4 OTH

AF:

0.274

Alfa

AF:

0.267

Hom.:

8981

Bravo

AF:

0.255

Asia WGS

AF:

0.406

AC:

1409

AN:

3478

EpiCase

AF:

0.273

EpiControl

AF:

0.285

ClinVar

Significance: Benign

Submissions summary: Benign:2Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 22479503) -

Spermatogenic failure 10

Other:1

Jan 01, 2012

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

8.3

DANN

Benign

0.53

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.71

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.71

Position offset: 3

DS_DL_spliceai

0.34

Position offset: -38

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over