rs200102944

Variant names:

• chr3-51830556-C-A
• ENST00000444293.5:c.110C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-51830556-C-A
• chr3-51830556-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442

Genes affected

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

ENSG00000285749 (HGNC:):

ACMG classification

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
IQCF3	NM_001393887.1	c.220C>A	p.Arg74Arg	synonymous_variant	Exon 3 of 3	ENST00000440739.4	NP_001380816.1
IQCF3	NM_001085479.3	c.220C>A	p.Arg74Arg	synonymous_variant	Exon 7 of 7		NP_001078948.1
IQCF3	NM_001207023.2	c.220C>A	p.Arg74Arg	synonymous_variant	Exon 7 of 7		NP_001193952.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IQCF3	ENST00000440739.4	c.220C>A	p.Arg74Arg	synonymous_variant	Exon 3 of 3	2	NM_001393887.1	ENSP00000402012.2
ENSG00000285749	ENST00000456080.5	c.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;