chr19-35269623-T-G
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3
The NM_003367.4(USF2):āc.152T>Gā(p.Ile51Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.0000067 ( 0 hom., cov: 29)
Exomes š: 0.0017 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
USF2
NM_003367.4 missense
NM_003367.4 missense
Scores
7
8
3
Clinical Significance
Conservation
PhyloP100: 3.53
Genes affected
USF2 (HGNC:12594): (upstream transcription factor 2, c-fos interacting) This gene encodes a member of the basic helix-loop-helix leucine zipper family of transcription factors. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs and is involved in regulating multiple cellular processes. [provided by RefSeq, Mar 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.817
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USF2 | NM_003367.4 | c.152T>G | p.Ile51Ser | missense_variant | 3/10 | ENST00000222305.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USF2 | ENST00000222305.8 | c.152T>G | p.Ile51Ser | missense_variant | 3/10 | 1 | NM_003367.4 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 150358Hom.: 0 Cov.: 29 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00170 AC: 2407AN: 1416758Hom.: 0 Cov.: 33 AF XY: 0.00157 AC XY: 1105AN XY: 705104
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000665 AC: 1AN: 150358Hom.: 0 Cov.: 29 AF XY: 0.0000136 AC XY: 1AN XY: 73350
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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 | May 15, 2023 | The c.152T>G (p.I51S) alteration is located in exon 3 (coding exon 3) of the USF2 gene. This alteration results from a T to G substitution at nucleotide position 152, causing the isoleucine (I) at amino acid position 51 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Pathogenic
D;D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;M;M;M;.
MutationTaster
Benign
D;D;N
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;N;.;N;.
REVEL
Pathogenic
Sift
Uncertain
D;D;.;D;.
Sift4G
Benign
T;D;D;T;D
Polyphen
D;D;.;.;D
Vest4
MutPred
0.42
.;.;.;.;Gain of disorder (P = 0.0034);
MVP
MPC
2.3
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.