Variant rs12146078 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017556.4(FBLIM1):c.542-11C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 1,610,146 control chromosomes in the GnomAD database, including 43,212 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.18 ( 2930 hom., cov: 30)

Exomes 𝑓: 0.23 ( 40282 hom. )

Consequence

FBLIM1
NM_017556.4 intron

Scores

Splicing: ADA: 0.00004923

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.141

Variant links:

Genes affected

FBLIM1 (HGNC:24686): (filamin binding LIM protein 1) This gene encodes a protein with an N-terminal filamin-binding domain, a central proline-rich domain, and, multiple C-terminal LIM domains. This protein localizes at cell junctions and may link cell adhesion structures to the actin cytoskeleton. This protein may be involved in the assembly and stabilization of actin-filaments and likely plays a role in modulating cell adhesion, cell morphology and cell motility. This protein also localizes to the nucleus and may affect cardiomyocyte differentiation after binding with the CSX/NKX2-5 transcription factor. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

FBLIM1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FBLIM1	NM_017556.4 linkuse as main transcript	c.542-11C>T		intron_variant		ENST00000375766.8	NP_060026.2	Q8WUP2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FBLIM1	ENST00000375766.8 linkuse as main transcript	c.542-11C>T		intron_variant		2	NM_017556.4	ENSP00000364921.3		Q8WUP2-1

Frequencies

GnomAD3 genomes

AF:

0.184

AC:

27891

AN:

151786

Hom.:

2925

Cov.:

show subpopulations

Gnomad AFR

AF:

0.105

Gnomad AMI

AF:

0.204

Gnomad AMR

AF:

0.245

Gnomad ASJ

AF:

0.196

Gnomad EAS

AF:

0.0764

Gnomad SAS

AF:

0.399

Gnomad FIN

AF:

0.152

Gnomad MID

AF:

0.197

Gnomad NFE

AF:

0.215

Gnomad OTH

AF:

0.196

GnomAD3 exomes

AF:

0.225

AC:

56135

AN:

249430

Hom.:

7347

AF XY:

0.234

AC XY:

31503

AN XY:

134908

show subpopulations

Gnomad AFR exome

AF:

0.102

Gnomad AMR exome

AF:

0.302

Gnomad ASJ exome

AF:

0.179

Gnomad EAS exome

AF:

0.0671

Gnomad SAS exome

AF:

0.390

Gnomad FIN exome

AF:

0.162

Gnomad NFE exome

AF:

0.216

Gnomad OTH exome

AF:

0.223

GnomAD4 exome

AF:

0.227

AC:

331144

AN:

1458238

Hom.:

40282

Cov.:

AF XY:

0.232

AC XY:

168422

AN XY:

725196

show subpopulations

Gnomad4 AFR exome

AF:

0.101

Gnomad4 AMR exome

AF:

0.295

Gnomad4 ASJ exome

AF:

0.182

Gnomad4 EAS exome

AF:

0.0768

Gnomad4 SAS exome

AF:

0.389

Gnomad4 FIN exome

AF:

0.169

Gnomad4 NFE exome

AF:

0.225

Gnomad4 OTH exome

AF:

0.217

GnomAD4 genome

AF:

0.184

AC:

27916

AN:

151908

Hom.:

2930

Cov.:

AF XY:

0.186

AC XY:

13802

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.105

Gnomad4 AMR

AF:

0.246

Gnomad4 ASJ

AF:

0.196

Gnomad4 EAS

AF:

0.0767

Gnomad4 SAS

AF:

0.399

Gnomad4 FIN

AF:

0.152

Gnomad4 NFE

AF:

0.215

Gnomad4 OTH

AF:

0.194

Alfa

AF:

0.199

Hom.:

652

Bravo

AF:

0.184

Asia WGS

AF:

0.209

AC:

727

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.4

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000049

dbscSNV1_RF

Benign

0.0020

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over