chr1-156567307-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_178229.5(IQGAP3):c.126-761C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 152,284 control chromosomes in the GnomAD database, including 70,692 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 0.96 ( 70692 hom., cov: 32)
Consequence
IQGAP3
NM_178229.5 intron
NM_178229.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.185
Publications
2 publications found
Genes affected
IQGAP3 (HGNC:20669): (IQ motif containing GTPase activating protein 3) Enables calmodulin binding activity and myosin VI light chain binding activity. Predicted to be involved in regulation of actin cytoskeleton organization. Predicted to act upstream of or within several processes, including intracellular signal transduction; positive regulation of macromolecule metabolic process; and positive regulation of mammary gland epithelial cell proliferation. Predicted to be located in cytosol. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IQGAP3 | NM_178229.5 | c.126-761C>T | intron_variant | Intron 2 of 37 | ENST00000361170.7 | NP_839943.3 | ||
IQGAP3 | XM_011509198.4 | c.141-761C>T | intron_variant | Intron 2 of 37 | XP_011507500.1 | |||
IQGAP3 | XM_047445990.1 | c.141-761C>T | intron_variant | Intron 2 of 37 | XP_047301946.1 | |||
IQGAP3 | XM_047445996.1 | c.126-761C>T | intron_variant | Intron 2 of 37 | XP_047301952.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.962 AC: 146352AN: 152166Hom.: 70644 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
146352
AN:
152166
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.962 AC: 146458AN: 152284Hom.: 70692 Cov.: 32 AF XY: 0.962 AC XY: 71623AN XY: 74464 show subpopulations
GnomAD4 genome
AF:
AC:
146458
AN:
152284
Hom.:
Cov.:
32
AF XY:
AC XY:
71623
AN XY:
74464
show subpopulations
African (AFR)
AF:
AC:
35942
AN:
41524
American (AMR)
AF:
AC:
15128
AN:
15304
Ashkenazi Jewish (ASJ)
AF:
AC:
3472
AN:
3472
East Asian (EAS)
AF:
AC:
5184
AN:
5184
South Asian (SAS)
AF:
AC:
4818
AN:
4826
European-Finnish (FIN)
AF:
AC:
10612
AN:
10612
Middle Eastern (MID)
AF:
AC:
293
AN:
294
European-Non Finnish (NFE)
AF:
AC:
68027
AN:
68044
Other (OTH)
AF:
AC:
2070
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
260
520
780
1040
1300
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
912
1824
2736
3648
4560
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3455
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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