NM_001110556.2:c.1613A>T

Variant names:

• chrX-154365214-T-A
• rs1557178932
• NM_001110556.2:c.1613A>T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001110556.2(FLNA):​c.1613A>T​(p.Tyr538Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 24)
• Consequence: FLNA NM_001110556.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.78

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.28976327).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FLNA	NM_001110556.2	c.1613A>T	p.Tyr538Phe	missense_variant	Exon 11 of 48	ENST00000369850.10	NP_001104026.1
FLNA	NM_001456.4	c.1613A>T	p.Tyr538Phe	missense_variant	Exon 11 of 47		NP_001447.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FLNA	ENST00000369850.10	c.1613A>T	p.Tyr538Phe	missense_variant	Exon 11 of 48	1	NM_001110556.2	ENSP00000358866.3

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 24

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.083
BayesDel_addAF	Benign	0.0073	T
BayesDel_noAF	Benign	-0.23
CADD	Benign	20
DANN	Benign	0.95
DEOGEN2	Uncertain	0.57	D;.;.;.;.
FATHMM_MKL	Benign	0.75	D
LIST_S2	Uncertain	0.95	D;D;.;D;D
M_CAP	Benign	0.083	D
MetaRNN	Benign	0.29	T;T;T;T;T
MetaSVM	Benign	-0.30	T
MutationAssessor	Benign	0.85	L;.;L;L;.
PrimateAI	Uncertain	0.56	T
PROVEAN	Benign	-1.8	N;.;N;N;.
REVEL	Uncertain	0.30
Sift	Benign	0.33	T;.;T;T;.
Sift4G	Benign	0.34	T;T;T;T;T
Polyphen		0.019	B;.;B;B;.
Vest4		0.26
MutPred		0.65		Loss of phosphorylation at Y538 (P = 0.0107);.;Loss of phosphorylation at Y538 (P = 0.0107);Loss of phosphorylation at Y538 (P = 0.0107);.;
MVP		0.89
MPC		0.48
ClinPred		0.65	D
GERP RS		4.2
Varity_R		0.61
gMVP		0.63

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

Other links and lift over

dbSNP: rs1557178932; hg19: chrX-153593582;