rs55907818

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001458.5(FLNC):c.850+18G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0853 in 1,613,974 control chromosomes in the GnomAD database, including 6,000 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.081 ( 515 hom., cov: 33)

Exomes 𝑓: 0.086 ( 5485 hom. )

Consequence

FLNC
NM_001458.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: -3.50

Variant links:

Genes affected

FLNC (HGNC:3756): (filamin C) This gene encodes one of three related filamin genes, specifically gamma filamin. These filamin proteins crosslink actin filaments into orthogonal networks in cortical cytoplasm and participate in the anchoring of membrane proteins for the actin cytoskeleton. Three functional domains exist in filamin: an N-terminal filamentous actin-binding domain, a C-terminal self-association domain, and a membrane glycoprotein-binding domain. Mutations in this gene are a cause of cardiopathy. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2022]

FLNC links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 7-128837566-G-A is Benign according to our data. Variant chr7-128837566-G-A is described in ClinVar as [Benign]. Clinvar id is 258154.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-128837566-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.086 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FLNC	NM_001458.5 link	c.850+18G>A		intron_variant	Intron 4 of 47	ENST00000325888.13	NP_001449.3	Q14315-1Q59H94
FLNC	NM_001127487.2 link	c.850+18G>A		intron_variant	Intron 4 of 46		NP_001120959.1	Q14315-2Q59H94

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FLNC	ENST00000325888.13 link	c.850+18G>A		intron_variant	Intron 4 of 47	1	NM_001458.5	ENSP00000327145.8		Q14315-1
FLNC	ENST00000346177.6 link	c.850+18G>A		intron_variant	Intron 4 of 46	1		ENSP00000344002.6		Q14315-2

Frequencies

GnomAD3 genomes

AF:

0.0808

AC:

12304

AN:

152192

Hom.:

517

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0805

Gnomad AMI

AF:

0.0789

Gnomad AMR

AF:

0.0504

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.0870

Gnomad SAS

AF:

0.0928

Gnomad FIN

AF:

0.0629

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0873

Gnomad OTH

AF:

0.0961

GnomAD3 exomes

AF:

0.0789

AC:

19679

AN:

249328

Hom.:

825

AF XY:

0.0808

AC XY:

10935

AN XY:

135358

show subpopulations

Gnomad AFR exome

AF:

0.0838

Gnomad AMR exome

AF:

0.0384

Gnomad ASJ exome

AF:

0.108

Gnomad EAS exome

AF:

0.0725

Gnomad SAS exome

AF:

0.0872

Gnomad FIN exome

AF:

0.0684

Gnomad NFE exome

AF:

0.0882

Gnomad OTH exome

AF:

0.0903

GnomAD4 exome

AF:

0.0858

AC:

125360

AN:

1461664

Hom.:

5485

Cov.:

AF XY:

0.0862

AC XY:

62649

AN XY:

727148

show subpopulations

Gnomad4 AFR exome

AF:

0.0826

Gnomad4 AMR exome

AF:

0.0420

Gnomad4 ASJ exome

AF:

0.105

Gnomad4 EAS exome

AF:

0.0942

Gnomad4 SAS exome

AF:

0.0879

Gnomad4 FIN exome

AF:

0.0711

Gnomad4 NFE exome

AF:

0.0874

Gnomad4 OTH exome

AF:

0.0859

GnomAD4 genome

AF:

0.0809

AC:

12315

AN:

152310

Hom.:

515

Cov.:

AF XY:

0.0792

AC XY:

5897

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.0804

Gnomad4 AMR

AF:

0.0502

Gnomad4 ASJ

AF:

0.114

Gnomad4 EAS

AF:

0.0872

Gnomad4 SAS

AF:

0.0931

Gnomad4 FIN

AF:

0.0629

Gnomad4 NFE

AF:

0.0873

Gnomad4 OTH

AF:

0.0984

Alfa

AF:

0.0880

Hom.:

155

Bravo

AF:

0.0803

Asia WGS

AF:

0.101

AC:

352

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:5

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Apr 04, 2023

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

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 08, 2016

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. -

Jan 08, 2016

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Myofibrillar myopathy 5;C3279722:Distal myopathy with posterior leg and anterior hand involvement;C4310749:Hypertrophic cardiomyopathy 26;CN239310:Dilated Cardiomyopathy, Dominant

Benign:1

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

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

-0.91

CADD

Benign

0.015

DANN

Benign

0.46

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