rs863223399
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_016097.5(IER3IP1):c.80delT(p.Phe27SerfsTer26) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000657 in 152,242 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016097.5 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IER3IP1 | ENST00000256433.6 | c.80delT | p.Phe27SerfsTer26 | frameshift_variant | Exon 1 of 3 | 1 | NM_016097.5 | ENSP00000256433.3 | ||
ENSG00000267228 | ENST00000588705.1 | n.80delT | non_coding_transcript_exon_variant | Exon 1 of 6 | 2 | ENSP00000465194.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152242Hom.: 0 Cov.: 34
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.92e-7 AC: 1AN: 1445498Hom.: 0 Cov.: 32 AF XY: 0.00000139 AC XY: 1AN XY: 717672
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152242Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
Microcephaly, epilepsy, and diabetes syndrome 1 Pathogenic:1
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Microcephaly, epilepsy, and diabetes syndrome Uncertain:1
This sequence change creates a premature translational stop signal (p.Phe27Serfs*26) in the IER3IP1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 56 amino acid(s) of the IER3IP1 protein. This variant is not present in population databases (ExAC no frequency). This premature translational stop signal has been observed in individual(s) with microcephaly, epilepsy, and diabetes syndrome (PMID: 24138066). This variant is also known as p.Phe27fsSer*25. ClinVar contains an entry for this variant (Variation ID: 208459). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at