19-680444-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_005860.3(FSTL3):​c.460C>A​(p.Arg154Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

FSTL3
NM_005860.3 missense

Scores

2
6
11

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.43
Variant links:
Genes affected
FSTL3 (HGNC:3973): (follistatin like 3) Follistatin-like 3 is a secreted glycoprotein of the follistatin-module-protein family. It may have a role in leukemogenesis. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FSTL3NM_005860.3 linkc.460C>A p.Arg154Ser missense_variant Exon 3 of 5 ENST00000166139.9 NP_005851.1 O95633-1A0A024R1Y8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FSTL3ENST00000166139.9 linkc.460C>A p.Arg154Ser missense_variant Exon 3 of 5 1 NM_005860.3 ENSP00000166139.3 O95633-1
FSTL3ENST00000589185.2 linkc.127C>A p.Arg43Ser missense_variant Exon 1 of 2 2 ENSP00000484376.1 A0A087X1Q2
FSTL3ENST00000592058.3 linkn.194C>A non_coding_transcript_exon_variant Exon 2 of 4 5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1111162
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
530406
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Feb 10, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.460C>A (p.R154S) alteration is located in exon 3 (coding exon 3) of the FSTL3 gene. This alteration results from a C to A substitution at nucleotide position 460, causing the arginine (R) at amino acid position 154 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.25
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.51
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.18
T;.
Eigen
Uncertain
0.38
Eigen_PC
Uncertain
0.35
FATHMM_MKL
Benign
0.31
N
LIST_S2
Benign
0.83
T;T
M_CAP
Pathogenic
0.71
D
MetaRNN
Uncertain
0.52
D;D
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.4
L;.
PrimateAI
Pathogenic
0.83
D
PROVEAN
Uncertain
-2.9
D;.
REVEL
Benign
0.086
Sift
Uncertain
0.0060
D;.
Sift4G
Benign
0.46
T;T
Polyphen
0.99
D;.
Vest4
0.25
MutPred
0.52
Loss of methylation at R154 (P = 0.0284);.;
MVP
0.76
MPC
1.0
ClinPred
0.99
D
GERP RS
3.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.66
gMVP
0.70

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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.

Other links and lift over

dbSNP: rs1367177915; hg19: chr19-680444; API