rs1472578
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001042706.3(IQCJ):c.9+21408T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 151,656 control chromosomes in the GnomAD database, including 25,889 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 0.55 ( 25889 hom., cov: 32)
Consequence
IQCJ
NM_001042706.3 intron
NM_001042706.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.353
Genes affected
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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=-0.96).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQCJ | NM_001042706.3 | c.9+21408T>A | intron_variant | ENST00000397832.7 | |||
IQCJ-SCHIP1 | NM_001197113.2 | c.9+21408T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQCJ | ENST00000397832.7 | c.9+21408T>A | intron_variant | 1 | NM_001042706.3 | ||||
IQCJ | ENST00000451172.5 | c.9+21408T>A | intron_variant | 1 | P1 | ||||
IQCJ | ENST00000482126.1 | c.9+21408T>A | intron_variant | 1 | |||||
IQCJ | ENST00000481796.1 | n.370+127552T>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.548 AC: 82975AN: 151538Hom.: 25880 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.547 AC: 82999AN: 151656Hom.: 25889 Cov.: 32 AF XY: 0.547 AC XY: 40580AN XY: 74132
GnomAD4 genome
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32
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40580
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74132
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Asia WGS
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1955
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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