rs200102944

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The ENST00000444293.5(IQCF3):​c.110C>A​(p.Thr37Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/14 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T37M) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

IQCF3
ENST00000444293.5 missense

Scores

1
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.442
Variant links:
Genes affected
IQCF3 (HGNC:31816): (IQ motif containing F3) Predicted to enable calmodulin binding activity. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.06983715).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IQCF3NM_001393887.1 linkc.220C>A p.Arg74Arg synonymous_variant Exon 3 of 3 ENST00000440739.4 NP_001380816.1
IQCF3NM_001085479.3 linkc.220C>A p.Arg74Arg synonymous_variant Exon 7 of 7 NP_001078948.1 P0C7M6
IQCF3NM_001207023.2 linkc.220C>A p.Arg74Arg synonymous_variant Exon 7 of 7 NP_001193952.1 P0C7M6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IQCF3ENST00000440739.4 linkc.220C>A p.Arg74Arg synonymous_variant Exon 3 of 3 2 NM_001393887.1 ENSP00000402012.2 P0C7M6
ENSG00000285749ENST00000456080.5 linkc.220C>A p.Arg74Arg synonymous_variant Exon 8 of 8 2 ENSP00000415609.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.29
T
BayesDel_noAF
Benign
-0.65
CADD
Benign
4.6
DANN
Benign
0.84
Eigen
Benign
-0.56
Eigen_PC
Benign
-0.74
FATHMM_MKL
Benign
0.028
N
M_CAP
Benign
0.0031
T
MetaRNN
Benign
0.070
T
MetaSVM
Benign
-0.96
T
PROVEAN
Benign
5.0
N
REVEL
Benign
0.12
Sift4G
Pathogenic
0.0
D
Vest4
0.12
MutPred
0.14
Gain of ubiquitination at T37 (P = 0.0039);
MVP
0.37
ClinPred
0.087
T
GERP RS
-0.86

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-51864572; API