chr15-90441492-G-GA
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_003870.4(IQGAP1):c.650-14_650-13insA variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000571 in 1,050,682 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000057 ( 0 hom. )
Consequence
IQGAP1
NM_003870.4 splice_polypyrimidine_tract, intron
NM_003870.4 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.255
Genes affected
IQGAP1 (HGNC:6110): (IQ motif containing GTPase activating protein 1) This gene encodes a member of the IQGAP family. The protein contains four IQ domains, one calponin homology domain, one Ras-GAP domain and one WW domain. It interacts with components of the cytoskeleton, with cell adhesion molecules, and with several signaling molecules to regulate cell morphology and motility. Expression of the protein is upregulated by gene amplification in two gastric cancer cell lines. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQGAP1 | NM_003870.4 | c.650-14_650-13insA | splice_polypyrimidine_tract_variant, intron_variant | ENST00000268182.10 | |||
IQGAP1 | XM_047433204.1 | c.650-14_650-13insA | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQGAP1 | ENST00000268182.10 | c.650-14_650-13insA | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003870.4 | P1 | |||
IQGAP1 | ENST00000560738.1 | c.107-24555_107-24554insA | intron_variant | 5 | |||||
IQGAP1 | ENST00000633485.1 | c.650-14_650-13insA | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
GnomAD4 exome AF: 0.00000571 AC: 6AN: 1050682Hom.: 0 Cov.: 28 AF XY: 0.00000573 AC XY: 3AN XY: 523354
GnomAD4 exome
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1050682
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28
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3
AN XY:
523354
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GnomAD4 genome ? Cov.: 31
GnomAD4 genome
?
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31
Bravo
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ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
CIC-DUX Sarcoma Other:1
not provided, no classification provided | literature only | Children's Cancer Therapy Development Institute | - | - - |
Computational scores
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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