chr5-1878995-A-AT
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_016358.3(IRX4):c.737-204_737-203insA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.25 ( 4632 hom., cov: 0)
Consequence
IRX4
NM_016358.3 intron
NM_016358.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.720
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 Benign. Variant got -10 ACMG points.
BP6
Variant 5-1878995-A-AT is Benign according to our data. Variant chr5-1878995-A-AT is described in ClinVar as [Benign]. Clinvar id is 1222896.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRX4 | NM_016358.3 | c.737-204_737-203insA | intron_variant | ENST00000231357.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRX4 | ENST00000231357.7 | c.737-204_737-203insA | intron_variant | 1 | NM_016358.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.251 AC: 36388AN: 145048Hom.: 4631 Cov.: 0
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.251 AC: 36393AN: 145074Hom.: 4632 Cov.: 0 AF XY: 0.252 AC XY: 17727AN XY: 70416
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70416
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at