5-1880777-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_016358.3(IRX4):c.355G>C(p.Ala119Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A119T) has been classified as Benign.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
IRX4
NM_016358.3 missense
NM_016358.3 missense
Scores
2
2
14
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.73
Genes affected
IRX4 (HGNC:6129): (iroquois homeobox 4) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in cell development; neuron differentiation; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within heart development. Predicted to be part of chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRX4 | NM_016358.3 | c.355G>C | p.Ala119Pro | missense_variant | 3/5 | ENST00000231357.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRX4 | ENST00000231357.7 | c.355G>C | p.Ala119Pro | missense_variant | 3/5 | 1 | NM_016358.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 151882Hom.: 0 Cov.: 31 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1461508Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727090
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GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 151882Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74186
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T;.;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D;D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N;N;N;.
MutationTaster
Benign
P;P;P
PrimateAI
Pathogenic
T
PROVEAN
Benign
N;N;.;.;N;N
REVEL
Benign
Sift
Benign
T;T;.;.;T;T
Sift4G
Benign
T;T;T;T;T;T
Polyphen
D;D;.;.;D;.
Vest4
MutPred
Gain of glycosylation at A119 (P = 0.0084);Gain of glycosylation at A119 (P = 0.0084);Gain of glycosylation at A119 (P = 0.0084);Gain of glycosylation at A119 (P = 0.0084);Gain of glycosylation at A119 (P = 0.0084);Gain of glycosylation at A119 (P = 0.0084);
MVP
MPC
0.78
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