2-48359081-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PP3_StrongBS2
The NM_002158.4(FOXN2):c.572C>T(p.Pro191Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000143 in 1,612,498 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000013 ( 0 hom. )
Consequence
FOXN2
NM_002158.4 missense
NM_002158.4 missense
Scores
11
5
1
Clinical Significance
Conservation
PhyloP100: 5.78
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.967
BS2
High AC in GnomAdExome4 at 19 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXN2 | NM_002158.4 | c.572C>T | p.Pro191Leu | missense_variant | 4/7 | ENST00000340553.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXN2 | ENST00000340553.8 | c.572C>T | p.Pro191Leu | missense_variant | 4/7 | 1 | NM_002158.4 | P1 | |
FOXN2 | ENST00000413569.5 | c.572C>T | p.Pro191Leu | missense_variant | 3/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000264 AC: 4AN: 151508Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251028Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135654
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GnomAD4 exome AF: 0.0000130 AC: 19AN: 1460990Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 726828
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GnomAD4 genome AF: 0.0000264 AC: 4AN: 151508Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74008
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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 | Nov 09, 2021 | The c.572C>T (p.P191L) alteration is located in exon 4 (coding exon 2) of the FOXN2 gene. This alteration results from a C to T substitution at nucleotide position 572, causing the proline (P) at amino acid position 191 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Pathogenic
D
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;.
REVEL
Pathogenic
Sift
Uncertain
D;D;.
Sift4G
Pathogenic
D;D;D
Polyphen
1.0
.;D;.
Vest4
0.91, 0.92
MutPred
Loss of disorder (P = 0.0516);Loss of disorder (P = 0.0516);.;
MVP
MPC
0.13
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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