rs31087
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000290552.8(IRX6):c.1333+15G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 1,582,520 control chromosomes in the GnomAD database, including 98,073 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.31 ( 7805 hom., cov: 32)
Exomes 𝑓: 0.35 ( 90268 hom. )
Consequence
IRX6
ENST00000290552.8 intron
ENST00000290552.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.254
Genes affected
IRX6 (HGNC:14675): (iroquois homeobox 6) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; DNA-binding transcription repressor 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, DNA-templated. Predicted to act upstream of or within detection of visible light; negative regulation of transcription, DNA-templated; and retina morphogenesis in camera-type eye. 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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IRX6 | NM_024335.3 | c.1333+15G>A | intron_variant | ENST00000290552.8 | NP_077311.2 | |||
IRX6 | XM_005256137.4 | c.1333+15G>A | intron_variant | XP_005256194.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IRX6 | ENST00000290552.8 | c.1333+15G>A | intron_variant | 1 | NM_024335.3 | ENSP00000290552 | P1 | |||
ENST00000558730.2 | n.88+4175C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.315 AC: 47808AN: 151904Hom.: 7804 Cov.: 32
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GnomAD3 exomes AF: 0.352 AC: 81466AN: 231570Hom.: 14574 AF XY: 0.353 AC XY: 44796AN XY: 127042
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GnomAD4 exome AF: 0.353 AC: 505194AN: 1430498Hom.: 90268 Cov.: 45 AF XY: 0.353 AC XY: 250181AN XY: 707986
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GnomAD4 genome AF: 0.315 AC: 47835AN: 152022Hom.: 7805 Cov.: 32 AF XY: 0.315 AC XY: 23430AN XY: 74298
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at