16-4780067-G-C

Position:

• chr16-4780067-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_144605.5(SEPTIN12):​c.727-281C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 151,540 control chromosomes in the GnomAD database, including 7,514 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.31 (7514 hom., cov: 30)
• Consequence: SEPTIN12 NM_144605.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.00

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]

ENSG00000285952 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BP6: Variant 16-4780067-G-C is Benign according to our data. Variant chr16-4780067-G-C is described in ClinVar as [Benign]. Clinvar id is 1228491.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEPTIN12	NM_144605.5	c.727-281C>G		intron_variant		ENST00000268231.13	NP_653206.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEPTIN12	ENST00000268231.13	c.727-281C>G		intron_variant		1	NM_144605.5	ENSP00000268231.8

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46584 AN: 151422 Hom.: 7484 Cov.: 30

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.308 AC: 46663 AN: 151540 Hom.: 7514 Cov.: 30 AF XY: 0.304 AC XY: 22541 AN XY: 74050

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.315

Alfa AF: 0.140 Hom.: 225

Bravo AF: 0.320

Asia WGS AF: 0.417 AC: 1449 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.24

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs8060334; hg19: chr16-4830068;