chrX-154362467-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_001110556.2(FLNA):c.2516C>T(p.Thr839Met) variant causes a missense change. The variant allele was found at a frequency of 0.000172 in 1,210,576 control chromosomes in the GnomAD database, including 1 homozygotes. There are 75 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T839A) has been classified as Benign.

Frequency

Genomes: 𝑓 0.00020 ( 0 hom., 10 hem., cov: 23)

Exomes 𝑓: 0.00017 ( 1 hom. 65 hem. )

Consequence

FLNA
NM_001110556.2 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 6.72

Publications

3 publications found

Variant links:

Genes affected

FLNA (HGNC:3754): (filamin A) The protein encoded by this gene is an actin-binding protein that crosslinks actin filaments and links actin filaments to membrane glycoproteins. The encoded protein is involved in remodeling the cytoskeleton to effect changes in cell shape and migration. This protein interacts with integrins, transmembrane receptor complexes, and second messengers. Defects in this gene are a cause of several syndromes, including periventricular nodular heterotopias (PVNH1, PVNH4), otopalatodigital syndromes (OPD1, OPD2), frontometaphyseal dysplasia (FMD), Melnick-Needles syndrome (MNS), and X-linked congenital idiopathic intestinal pseudoobstruction (CIIPX). Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2009]

FLNA Gene-Disease associations (from GenCC):

periventricular nodular heterotopia
Inheritance: AD, XL Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
frontometaphyseal dysplasia 1
Inheritance: XL Classification: DEFINITIVE Submitted by: G2P
genetic developmental and epileptic encephalopathy
Inheritance: XL Classification: DEFINITIVE Submitted by: G2P
heterotopia, periventricular, X-linked dominant
Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Illumina
intestinal pseudoobstruction, neuronal, chronic idiopathic, X-linked
Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
Melnick-Needles syndrome
Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae)
otopalatodigital syndrome type 2
Inheritance: XL Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet, G2P, Labcorp Genetics (formerly Invitae)
terminal osseous dysplasia-pigmentary defects syndrome
Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae)
cardiac valvular dysplasia, X-linked
Inheritance: XL Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae)
frontometaphyseal dysplasia
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
congenital short bowel syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
otopalatodigital syndrome type 1
Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
X-linked Ehlers-Danlos syndrome
Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
familial thoracic aortic aneurysm and aortic dissection
Inheritance: XL Classification: LIMITED Submitted by: ClinGen

FLNA links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.04887998).

BP6

Variant X-154362467-G-A is Benign according to our data. Variant chrX-154362467-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 213441.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154362467-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 213441.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154362467-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 213441.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154362467-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 213441.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154362467-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 213441.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154362467-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 213441.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154362467-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 213441.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154362467-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 213441.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154362467-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 213441.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154362467-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 213441.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154362467-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 213441.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154362467-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 213441.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154362467-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 213441.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154362467-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 213441.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154362467-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 213441.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154362467-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 213441.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154362467-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 213441.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Hemizygotes in GnomAd4 at 10 XL,AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FLNA	NM_001110556.2 link	c.2516C>T	p.Thr839Met	missense_variant	Exon 17 of 48	ENST00000369850.10	NP_001104026.1	P21333-1Q60FE5Q6NXF2
FLNA	NM_001456.4 link	c.2516C>T	p.Thr839Met	missense_variant	Exon 17 of 47		NP_001447.2	P21333-2Q60FE5Q6NXF2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FLNA	ENST00000369850.10 link	c.2516C>T	p.Thr839Met	missense_variant	Exon 17 of 48	1	NM_001110556.2	ENSP00000358866.3		P21333-1

Frequencies

GnomAD3 genomes

AF:

0.000203

AC:

AN:

113151

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000321

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00829

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000331

AC:

AN:

181269

AF XY:

0.000311

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000146

Gnomad ASJ exome

AF:

0.00683

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000617

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000169

AC:

185

AN:

1097425

Hom.:

Cov.:

AF XY:

0.000179

AC XY:

AN XY:

363033

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

26394

American (AMR)

AF:

0.000114

AC:

AN:

35205

Ashkenazi Jewish (ASJ)

AF:

0.00717

AC:

139

AN:

19383

East Asian (EAS)

AF:

0.00

AC:

AN:

30203

South Asian (SAS)

AF:

0.0000554

AC:

AN:

54142

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40091

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4134

European-Non Finnish (NFE)

AF:

0.0000238

AC:

AN:

841798

Other (OTH)

AF:

0.000412

AC:

AN:

46075

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

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:

0.000203

AC:

AN:

113151

Hom.:

Cov.:

AF XY:

0.000283

AC XY:

AN XY:

35283

show subpopulations

African (AFR)

AF:

0.0000321

AC:

AN:

31196

American (AMR)

AF:

0.00

AC:

AN:

10811

Ashkenazi Jewish (ASJ)

AF:

0.00829

AC:

AN:

2655

East Asian (EAS)

AF:

0.00

AC:

AN:

3604

South Asian (SAS)

AF:

0.00

AC:

AN:

2792

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6316

Middle Eastern (MID)

AF:

0.00

AC:

AN:

240

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

53313

Other (OTH)

AF:

0.00

AC:

AN:

1537

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome 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

Alfa

AF:

0.000816

Hom.:

Bravo

AF:

0.000166

ESP6500AA

AF:

0.000282

AC:

ESP6500EA

AF:

0.000765

AC:

ExAC

AF:

0.000165

AC:

EpiCase

AF:

0.0000545

EpiControl

AF:

0.00

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Familial thoracic aortic aneurysm and aortic dissection

Benign:1

May 11, 2017

Ambry Genetics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This alteration is classified as 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. -

Melnick-Needles syndrome;C0265293:Frontometaphyseal dysplasia;C1844696:Oto-palato-digital syndrome, type II;C1848213:Heterotopia, periventricular, X-linked dominant

Benign:1

Jan 01, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Nov 13, 2020

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Has not been previously published as pathogenic or benign to our knowledge -

Melnick-Needles syndrome;C0262436:Cardiac valvular dysplasia, X-linked;C0265251:Oto-palato-digital syndrome, type I;C1844696:Oto-palato-digital syndrome, type II;C1845902:FG syndrome 2;C1846129:Terminal osseous dysplasia-pigmentary defects syndrome;C1848213:Heterotopia, periventricular, X-linked dominant;C2746068:Intestinal pseudoobstruction, neuronal, chronic idiopathic, X-linked;C4281559:Frontometaphyseal dysplasia 1

Benign:1

Aug 09, 2021

Fulgent Genetics, Fulgent Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

FLNA-related disorder

Benign:1

Jun 10, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.070

BayesDel_addAF

Benign

-0.067

BayesDel_noAF

Uncertain

-0.080

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.77

D;.;.;.;.

FATHMM_MKL

Uncertain

0.90

LIST_S2

Uncertain

0.93

D;D;.;D;D

M_CAP

Benign

0.023

MetaRNN

Benign

0.049

T;T;T;T;T

MetaSVM

Benign

-0.48

MutationAssessor

Uncertain

2.4

M;.;M;M;.

PhyloP100

6.7

PrimateAI

Uncertain

0.71

PROVEAN

Uncertain

-2.8

D;.;D;D;.

REVEL

Uncertain

0.33

Sift

Benign

0.077

T;.;T;T;.

Sift4G

Benign

0.14

T;T;T;T;T

Polyphen

0.88

P;.;B;B;.

Vest4

0.71

MVP

0.84

MPC

0.74

ClinPred

0.046

GERP RS

4.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

Varity_R

0.23

gMVP

0.44

Mutation Taster

=96/4

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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