9-128608264-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_001130438.3(SPTAN1):c.4479G>A(p.Ala1493Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,614,150 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A1493A) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.000033 ( 0 hom., cov: 31)

Exomes 𝑓: 0.000014 ( 1 hom. )

Consequence

SPTAN1
NM_001130438.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.397

Publications

1 publications found

Variant links:

Genes affected

SPTAN1 (HGNC:11273): (spectrin alpha, non-erythrocytic 1) Spectrins are a family of filamentous cytoskeletal proteins that function as essential scaffold proteins that stabilize the plasma membrane and organize intracellular organelles. Spectrins are composed of alpha and beta dimers that associate to form tetramers linked in a head-to-head arrangement. This gene encodes an alpha spectrin that is specifically expressed in nonerythrocytic cells. The encoded protein has been implicated in other cellular functions including DNA repair and cell cycle regulation. Mutations in this gene are the cause of early infantile epileptic encephalopathy-5. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Sep 2010]

SPTAN1 Gene-Disease associations (from GenCC):

developmental and epileptic encephalopathy, 5
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine
genetic developmental and epileptic encephalopathy
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
infantile spasms
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

SPTAN1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP6

Variant 9-128608264-G-A is Benign according to our data. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128608264-G-A is described in CliVar as Likely_benign. Clinvar id is 586678.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.397 with no splicing effect.

BS2

High AC in GnomAd4 at 5 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPTAN1	NM_001130438.3 link	c.4479G>A	p.Ala1493Ala	synonymous_variant	Exon 34 of 57	ENST00000372739.7	NP_001123910.1	Q13813-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPTAN1	ENST00000372739.7 link	c.4479G>A	p.Ala1493Ala	synonymous_variant	Exon 34 of 57	1	NM_001130438.3	ENSP00000361824.4		Q13813-2

Frequencies

GnomAD3 genomes

AF:

0.0000329

AC:

AN:

152150

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000588

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000239

AC:

AN:

251418

AF XY:

0.0000368

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000176

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000137

AC:

AN:

1461882

Hom.:

Cov.:

AF XY:

0.0000206

AC XY:

AN XY:

727240

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33480

American (AMR)

AF:

0.00

AC:

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26136

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.0000927

AC:

AN:

86256

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53410

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.00000899

AC:

AN:

1112012

Other (OTH)

AF:

0.0000331

AC:

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000328

AC:

AN:

152268

Hom.:

Cov.:

AF XY:

0.0000403

AC XY:

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.0000241

AC:

AN:

41546

American (AMR)

AF:

0.00

AC:

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.00

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0000588

AC:

AN:

68032

Other (OTH)

AF:

0.00

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.545

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0000330

Hom.:

Bravo

AF:

0.0000151

EpiCase

AF:

0.0000545

EpiControl

AF:

0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Developmental and epileptic encephalopathy

Benign:1

Feb 12, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Jun 20, 2018

Athena Diagnostics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

3.7

(source)

DANN

Benign

0.32

PhyloP100

-0.40

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over