Variant 17-77307216-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001113491.2(SEPTIN9):c.76+19T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.865 in 1,610,688 control chromosomes in the GnomAD database, including 603,506 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.88 ( 59077 hom., cov: 33)

Exomes 𝑓: 0.86 ( 544429 hom. )

Consequence

SEPTIN9
NM_001113491.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0360

Variant links:

Genes affected

SEPTIN9 (HGNC:7323): (septin 9) This gene is a member of the septin family involved in cytokinesis and cell cycle control. This gene is a candidate for the ovarian tumor suppressor gene. Mutations in this gene cause hereditary neuralgic amyotrophy, also known as neuritis with brachial predilection. A chromosomal translocation involving this gene on chromosome 17 and the MLL gene on chromosome 11 results in acute myelomonocytic leukemia. Multiple alternatively spliced transcript variants encoding different isoforms have been described.[provided by RefSeq, Mar 2009]

SEPTIN9 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 17-77307216-T-C is Benign according to our data. Variant chr17-77307216-T-C is described in ClinVar as [Benign]. Clinvar id is 518264.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-77307216-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
SEPTIN9	NM_001113491.2 linkuse as main transcript	c.76+19T>C	intron_variant	ENST00000427177.6
SEPTIN9	NM_001113492.2 linkuse as main transcript	c.-417+19T>C	intron_variant
SEPTIN9	NM_001293695.2 linkuse as main transcript	c.19+25662T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEPTIN9	ENST00000427177.6 linkuse as main transcript	c.76+19T>C		intron_variant		1	NM_001113491.2	A1	Q9UHD8-1

Frequencies

GnomAD3 genomes

AF:

0.880

AC:

133857

AN:

152142

Hom.:

59014

Cov.:

show subpopulations

Gnomad AFR

AF:

0.909

Gnomad AMI

AF:

0.925

Gnomad AMR

AF:

0.877

Gnomad ASJ

AF:

0.768

Gnomad EAS

AF:

0.987

Gnomad SAS

AF:

0.929

Gnomad FIN

AF:

0.916

Gnomad MID

AF:

0.858

Gnomad NFE

AF:

0.852

Gnomad OTH

AF:

0.852

GnomAD3 exomes

AF:

0.885

AC:

219534

AN:

248028

Hom.:

97502

AF XY:

0.884

AC XY:

119250

AN XY:

134922

show subpopulations

Gnomad AFR exome

AF:

0.907

Gnomad AMR exome

AF:

0.913

Gnomad ASJ exome

AF:

0.751

Gnomad EAS exome

AF:

0.989

Gnomad SAS exome

AF:

0.936

Gnomad FIN exome

AF:

0.916

Gnomad NFE exome

AF:

0.850

Gnomad OTH exome

AF:

0.863

GnomAD4 exome

AF:

0.863

AC:

1258711

AN:

1458428

Hom.:

544429

Cov.:

AF XY:

0.865

AC XY:

627670

AN XY:

725698

show subpopulations

Gnomad4 AFR exome

AF:

0.910

Gnomad4 AMR exome

AF:

0.908

Gnomad4 ASJ exome

AF:

0.756

Gnomad4 EAS exome

AF:

0.983

Gnomad4 SAS exome

AF:

0.935

Gnomad4 FIN exome

AF:

0.915

Gnomad4 NFE exome

AF:

0.850

Gnomad4 OTH exome

AF:

0.859

GnomAD4 genome

AF:

0.880

AC:

133983

AN:

152260

Hom.:

59077

Cov.:

AF XY:

0.884

AC XY:

65794

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.909

Gnomad4 AMR

AF:

0.877

Gnomad4 ASJ

AF:

0.768

Gnomad4 EAS

AF:

0.987

Gnomad4 SAS

AF:

0.930

Gnomad4 FIN

AF:

0.916

Gnomad4 NFE

AF:

0.852

Gnomad4 OTH

AF:

0.854

Alfa

AF:

0.857

Hom.:

9488

Bravo

AF:

0.875

Asia WGS

AF:

0.958

AC:

3332

AN:

3478

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

GeneDx

Jul 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.8

DANN

Benign

0.42

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