rs6658700
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000359942.8(IPP):c.1652-73G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 811,234 control chromosomes in the GnomAD database, including 36,995 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 0.28 ( 6236 hom., cov: 32)
Exomes 𝑓: 0.30 ( 30759 hom. )
Consequence
IPP
ENST00000359942.8 intron
ENST00000359942.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.250
Genes affected
IPP (HGNC:6108): (intracisternal A particle-promoted polypeptide) The protein encoded by this gene is a member of the kelch family of proteins, which is characterized by a 50 amino acid repeat which interacts with actin. Transcript variants have been described but their full-length nature has not been determined. [provided by RefSeq, Jul 2008]
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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=-0.69).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IPP | NM_001145349.2 | c.1652-73G>A | intron_variant | ||||
IPP | XM_047419673.1 | c.1652-73G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IPP | ENST00000359942.8 | c.1652-73G>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.283 AC: 43032AN: 151888Hom.: 6216 Cov.: 32
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GnomAD4 exome AF: 0.303 AC: 199511AN: 659228Hom.: 30759 Cov.: 9 AF XY: 0.305 AC XY: 106834AN XY: 349810
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GnomAD4 genome ? AF: 0.283 AC: 43091AN: 152006Hom.: 6236 Cov.: 32 AF XY: 0.284 AC XY: 21086AN XY: 74274
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at