chr9-128632648-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_001130438.3(SPTAN1):c.7090C>T(p.Leu2364Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,613,958 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)

Exomes 𝑓: 0.000034 ( 0 hom. )

Consequence

SPTAN1
NM_001130438.3 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 2.57

Publications

0 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 -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BP6

Variant 9-128632648-C-T is Benign according to our data. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128632648-C-T is described in CliVar as Benign/Likely_benign. Clinvar id is 238541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.57 with no splicing effect.

BS2

High AC in GnomAdExome4 at 49 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPTAN1	NM_001130438.3 link	c.7090C>T	p.Leu2364Leu	synonymous_variant	Exon 55 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.7090C>T	p.Leu2364Leu	synonymous_variant	Exon 55 of 57	1	NM_001130438.3	ENSP00000361824.4		Q13813-2

Frequencies

GnomAD3 genomes

AF:

0.0000197

AC:

AN:

152198

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000482

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:

0.0000147

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000239

AC:

AN:

251392

AF XY:

0.0000294

show subpopulations

Gnomad AFR exome

AF:

0.000185

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:

0.0000264

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000335

AC:

AN:

1461760

Hom.:

Cov.:

AF XY:

0.0000303

AC XY:

AN XY:

727180

show subpopulations

African (AFR)

AF:

0.0000299

AC:

AN:

33480

American (AMR)

AF:

0.00

AC:

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26134

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.00

AC:

AN:

86258

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53298

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.0000414

AC:

AN:

1112006

Other (OTH)

AF:

0.0000331

AC:

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.0000197

AC:

AN:

152198

Hom.:

Cov.:

AF XY:

0.0000269

AC XY:

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.0000482

AC:

AN:

41456

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:

5184

South Asian (SAS)

AF:

0.00

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10624

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.0000147

AC:

AN:

68030

Other (OTH)

AF:

0.00

AC:

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

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

Alfa

AF:

0.0000386

Hom.:

Bravo

AF:

0.0000340

EpiCase

AF:

0.0000545

EpiControl

AF:

0.0000593

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Apr 09, 2015

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Inborn genetic diseases

Benign:1

Jul 31, 2019

Ambry Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Developmental and epileptic encephalopathy

Benign:1

Jun 24, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Developmental and epileptic encephalopathy, 5

Benign:1

Jul 15, 2021

Genome-Nilou Lab

Significance: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

-0.36

CADD

Benign

(source)

DANN

Benign

0.86

PhyloP100

2.6

PromoterAI

-0.0058

Neutral

(source)

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

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over