chr5-76588909-G-A
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_006633.5(IQGAP2):c.462G>A(p.Leu154=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 1,583,014 control chromosomes in the GnomAD database, including 214,341 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.57 ( 25514 hom., cov: 32)
Exomes 𝑓: 0.50 ( 188827 hom. )
Consequence
IQGAP2
NM_006633.5 synonymous
NM_006633.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.113
Genes affected
IQGAP2 (HGNC:6111): (IQ motif containing GTPase activating protein 2) This gene encodes a member of the IQGAP family. The encoded protein contains three IQ domains, one calponin homology domain, one Ras-GAP domain and one WW domain. This protein interacts with components of the cytoskeleton, with cell adhesion molecules, and with several signaling molecules to regulate cell morphology and motility. It also acts as a tumor suppressor and has been found to play a role in regulating innate antiviral responses. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 5-76588909-G-A is Benign according to our data. Variant chr5-76588909-G-A is described in ClinVar as [Benign]. Clinvar id is 1232742.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.113 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IQGAP2 | NM_006633.5 | c.462G>A | p.Leu154= | synonymous_variant | 6/36 | ENST00000274364.11 | NP_006624.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IQGAP2 | ENST00000274364.11 | c.462G>A | p.Leu154= | synonymous_variant | 6/36 | 1 | NM_006633.5 | ENSP00000274364 | P1 | |
IQGAP2 | ENST00000514350.5 | c.381G>A | p.Leu127= | synonymous_variant | 6/22 | 1 | ENSP00000423672 | |||
IQGAP2 | ENST00000379730.7 | c.312G>A | p.Leu104= | synonymous_variant | 5/35 | 5 | ENSP00000442313 |
Frequencies
GnomAD3 genomes AF: 0.568 AC: 86293AN: 151880Hom.: 25495 Cov.: 32
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GnomAD3 exomes AF: 0.575 AC: 142563AN: 247978Hom.: 42971 AF XY: 0.572 AC XY: 76757AN XY: 134108
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GnomAD4 exome AF: 0.503 AC: 720501AN: 1431016Hom.: 188827 Cov.: 25 AF XY: 0.509 AC XY: 362999AN XY: 713668
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GnomAD4 genome AF: 0.568 AC: 86365AN: 151998Hom.: 25514 Cov.: 32 AF XY: 0.572 AC XY: 42523AN XY: 74304
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 11, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at