Variant chr7-35903153-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_001788.6(SEPTIN7):c.1212C>T(p.Phe404Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0163 in 152,064 control chromosomes in the GnomAD database, including 71 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.016 ( 71 hom., cov: 31)

Exomes 𝑓: 0.0057 ( 265 hom. )

Failed GnomAD Quality Control

Consequence

SEPTIN7
NM_001788.6 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.68

Variant links:

Genes affected

SEPTIN7 (HGNC:1717): (septin 7) This gene encodes a protein that is highly similar to the CDC10 protein of Saccharomyces cerevisiae. The protein also shares similarity with Diff 6 of Drosophila and with H5 of mouse. Each of these similar proteins, including the yeast CDC10, contains a GTP-binding motif. The yeast CDC10 protein is a structural component of the 10 nm filament which lies inside the cytoplasmic membrane and is essential for cytokinesis. This human protein functions in gliomagenesis and in the suppression of glioma cell growth, and it is required for the association of centromere-associated protein E with the kinetochore. Alternative splicing results in multiple transcript variants. Several related pseudogenes have been identified on chromosomes 5, 7, 9, 10, 11, 14, 17 and 19. [provided by RefSeq, Jul 2011]

SEPTIN7 links:

SEPTIN7 (HGNC:):

SEPTIN7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.31).

BP6

Variant 7-35903153-C-T is Benign according to our data. Variant chr7-35903153-C-T is described in ClinVar as [Benign]. Clinvar id is 769709.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=2.68 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEPTIN7	NM_001788.6 linkuse as main transcript	c.1212C>T	p.Phe404Phe	synonymous_variant	13/14	ENST00000350320.11	NP_001779.3	Q16181-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SEPTIN7	ENST00000350320.11 linkuse as main transcript	c.1212C>T	p.Phe404Phe	synonymous_variant	13/14	5	NM_001788.6	ENSP00000344868.8	Q16181-1E7EPK1
SEPTIN7	ENST00000635175.1 linkuse as main transcript	n.*1129C>T		non_coding_transcript_exon_variant	13/14	2		ENSP00000489192.1	A0A0U1RQW0
SEPTIN7	ENST00000635175.1 linkuse as main transcript	n.*1129C>T		3_prime_UTR_variant	13/14	2		ENSP00000489192.1	A0A0U1RQW0

Frequencies

GnomAD3 genomes

AF:

0.0163

AC:

2471

AN:

151946

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00411

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.0628

Gnomad ASJ

AF:

0.00404

Gnomad EAS

AF:

0.0405

Gnomad SAS

AF:

0.00872

Gnomad FIN

AF:

0.00284

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0149

Gnomad OTH

AF:

0.0120

GnomAD3 exomes

AF:

0.00628

AC:

1453

AN:

231458

Hom.:

AF XY:

0.00557

AC XY:

702

AN XY:

125922

show subpopulations

Gnomad AFR exome

AF:

0.00102

Gnomad AMR exome

AF:

0.0318

Gnomad ASJ exome

AF:

0.000916

Gnomad EAS exome

AF:

0.0141

Gnomad SAS exome

AF:

0.000766

Gnomad FIN exome

AF:

0.0000945

Gnomad NFE exome

AF:

0.00236

Gnomad OTH exome

AF:

0.00492

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00569

AC:

8122

AN:

1427568

Hom.:

265

Cov.:

AF XY:

0.00565

AC XY:

4014

AN XY:

710380

show subpopulations

Gnomad4 AFR exome

AF:

0.00171

Gnomad4 AMR exome

AF:

0.0442

Gnomad4 ASJ exome

AF:

0.00213

Gnomad4 EAS exome

AF:

0.0404

Gnomad4 SAS exome

AF:

0.00245

Gnomad4 FIN exome

AF:

0.00244

Gnomad4 NFE exome

AF:

0.00369

Gnomad4 OTH exome

AF:

0.00652

GnomAD4 genome

AF:

0.0163

AC:

2479

AN:

152064

Hom.:

Cov.:

AF XY:

0.0159

AC XY:

1180

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.00410

Gnomad4 AMR

AF:

0.0632

Gnomad4 ASJ

AF:

0.00404

Gnomad4 EAS

AF:

0.0404

Gnomad4 SAS

AF:

0.00872

Gnomad4 FIN

AF:

0.00284

Gnomad4 NFE

AF:

0.0149

Gnomad4 OTH

AF:

0.0118

Alfa

AF:

0.00992

Hom.:

Bravo

AF:

0.0241

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.31

CADD

Benign

DANN

Benign

0.71

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

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