rs200102944

Variant names:

• chr3-51830556-C-A
• rs200102944
• 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. The variant received 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. 13/17 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
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444293.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IQCF3	NM_001393887.1	MANE Select	c.220C>A	p.Arg74Arg	synonymous	Exon 3 of 3	NP_001380816.1	P0C7M6
	IQCF3	NM_001085479.3		c.220C>A	p.Arg74Arg	synonymous	Exon 7 of 7	NP_001078948.1	P0C7M6
	IQCF3	NM_001207023.2		c.220C>A	p.Arg74Arg	synonymous	Exon 7 of 7	NP_001193952.1	P0C7M6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IQCF3	ENST00000444293.5	TSL:1	c.110C>A	p.Thr37Lys	missense	Exon 3 of 3	ENSP00000402530.1	F2Z334
	IQCF3	ENST00000440739.4	TSL:2 MANE Select	c.220C>A	p.Arg74Arg	synonymous	Exon 3 of 3	ENSP00000402012.2	P0C7M6
	IQCF3	ENST00000437810.7	TSL:1	c.220C>A	p.Arg74Arg	synonymous	Exon 7 of 7	ENSP00000409373.2	P0C7M6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.41
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
PhyloP100		-0.44
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
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs200102944; hg19: chr3-51864572;