rs1534446
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001130700.2(IPCEF1):c.-61-14302A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 147,242 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000014 ( 0 hom., cov: 31)
Consequence
IPCEF1
NM_001130700.2 intron
NM_001130700.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.308
Genes affected
IPCEF1 (HGNC:21204): (interaction protein for cytohesin exchange factors 1) Predicted to enable peroxidase activity. Predicted to be involved in response to oxidative stress. Predicted to be located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IPCEF1 | NM_001130700.2 | c.-61-14302A>G | intron_variant | ENST00000367220.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IPCEF1 | ENST00000367220.9 | c.-61-14302A>G | intron_variant | 2 | NM_001130700.2 | A2 | |||
IPCEF1 | ENST00000265198.8 | c.-61-14302A>G | intron_variant | 1 | A2 | ||||
IPCEF1 | ENST00000422970.6 | c.-62+2637A>G | intron_variant | 1 | A2 | ||||
IPCEF1 | ENST00000520261.1 | c.-62+2637A>G | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000136 AC: 2AN: 147242Hom.: 0 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0000136 AC: 2AN: 147242Hom.: 0 Cov.: 31 AF XY: 0.0000278 AC XY: 2AN XY: 71828
GnomAD4 genome
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71828
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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