NM_001110556.2(FLNA):c.7267C>T (p.Pro2423Ser) AND not specified

Germline classification:: Likely benign (3 submissions)
Last evaluated:: Apr 16, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000197144.19

Allele description [Variation Report for NM_001110556.2(FLNA):c.7267C>T (p.Pro2423Ser)]

NM_001110556.2(FLNA):c.7267C>T (p.Pro2423Ser)

Gene:

FLNA:filamin A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

NM_001110556.2(FLNA):c.7267C>T (p.Pro2423Ser)

Other names:

p.P2415S:CCT>TCT

HGVS:

NC_000023.11:g.154350097G>A
NG_011506.2:g.29542C>T
NM_001110556.2:c.7267C>TMANE SELECT
NM_001456.4:c.7243C>T
NP_001104026.1:p.Pro2423Ser
NP_001447.2:p.Pro2415Ser
NP_001447.2:p.Pro2415Ser
LRG_1340t1:c.7267C>T
LRG_1340:g.29542C>T
LRG_1340p1:p.Pro2423Ser
NC_000023.10:g.153578465G>A
NM_001110556.1:c.7267C>T
NM_001456.3:c.7243C>T

Protein change:

P2415S

Links:

dbSNP: rs200198847

NCBI 1000 Genomes Browser:

rs200198847

Molecular consequence:

NM_001110556.2:c.7267C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001456.4:c.7243C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000856324	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Likely benign (Aug 22, 2017)	germline	clinical testing	Citation Link,
SCV003839544	Genetic Services Laboratory, University of Chicago	no assertion criteria provided	Likely benign (Dec 14, 2022)	germline	clinical testing
SCV005076136	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (Apr 16, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000856324

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Likely benign
(Aug 22, 2017)

germline

clinical testing

Citation Link,

SCV003839544

Genetic Services Laboratory, University of Chicago

no assertion criteria provided

Likely benign
(Dec 14, 2022)

germline

clinical testing

SCV005076136

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely benign
(Apr 16, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000856324.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		1	not provided	not provided	not provided

From Genetic Services Laboratory, University of Chicago, SCV003839544.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV005076136.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Variant summary: FLNA c.7267C>T (p.Pro2423Ser) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00043 in 181695 control chromosomes. The observed variant frequency is approximately 1400 fold of the estimated maximal expected allele frequency for a pathogenic variant in FLNA causing Periventricular Nodular Heterotopia phenotype (3.1e-07), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.7267C>T in individuals affected with Periventricular Nodular Heterotopia and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 213485). Based on the evidence outlined above, the variant was classified as likely benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 24, 2024

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