chr4-161386198-T-C
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020116.5(FSTL5):āc.2093A>Gā(p.Tyr698Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000266 in 1,613,812 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000020 ( 0 hom., cov: 32)
Exomes š: 0.000027 ( 0 hom. )
Consequence
FSTL5
NM_020116.5 missense
NM_020116.5 missense
Scores
5
5
9
Clinical Significance
Conservation
PhyloP100: 5.78
Genes affected
FSTL5 (HGNC:21386): (follistatin like 5) Predicted to enable calcium ion binding activity. Predicted to be involved in cell differentiation. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
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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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FSTL5 | NM_020116.5 | c.2093A>G | p.Tyr698Cys | missense_variant | 16/16 | ENST00000306100.10 | NP_064501.2 | |
FSTL5 | NM_001128427.3 | c.2090A>G | p.Tyr697Cys | missense_variant | 16/16 | NP_001121899.1 | ||
FSTL5 | NM_001128428.3 | c.2063A>G | p.Tyr688Cys | missense_variant | 15/15 | NP_001121900.1 | ||
FSTL5 | XM_011532126.1 | c.2066A>G | p.Tyr689Cys | missense_variant | 15/15 | XP_011530428.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FSTL5 | ENST00000306100.10 | c.2093A>G | p.Tyr698Cys | missense_variant | 16/16 | 1 | NM_020116.5 | ENSP00000305334 | P5 | |
FSTL5 | ENST00000379164.8 | c.2090A>G | p.Tyr697Cys | missense_variant | 16/16 | 1 | ENSP00000368462 | A1 | ||
FSTL5 | ENST00000427802.2 | c.2063A>G | p.Tyr688Cys | missense_variant | 15/15 | 1 | ENSP00000389270 | A1 | ||
ENST00000508189.1 | n.621T>C | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152040Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250738Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135468
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GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461772Hom.: 0 Cov.: 33 AF XY: 0.0000206 AC XY: 15AN XY: 727178
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152040Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74242
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2023 | The c.2093A>G (p.Y698C) alteration is located in exon 16 (coding exon 15) of the FSTL5 gene. This alteration results from a A to G substitution at nucleotide position 2093, causing the tyrosine (Y) at amino acid position 698 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
PROVEAN
Pathogenic
D;D;D
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;D;D
Polyphen
D;.;.
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at