3-159090849-T-A

Variant names:

• chr3-159090849-T-A
• rs1472578
• NM_001042706.3:c.9+21408T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001042706.3(IQCJ):​c.9+21408T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 151,656 control chromosomes in the GnomAD database, including 25,889 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 0.55 (25889 hom., cov: 32)
• Consequence: IQCJ NM_001042706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353
• Publications: 5 publications found

Genes affected

IQCJ (HGNC:32406): (IQ motif containing J)

IQCJ-SCHIP1 (HGNC:38842): (IQCJ-SCHIP1 readthrough) This locus represents naturally occurring read-through transcription from the neighboring IQ motif containing J (IQCJ) and schwannomin interacting protein 1 (SCHIP1) genes. Alternative splicing results in multiple transcript variants that are composed of in-frame exons from each individual gene. The resulting fusion products are thought to be components of the multimolecular complexes of axon initial segments and nodes of Ranvier, and they may play a role in calcium-mediated responses. [provided by RefSeq, Oct 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001042706.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IQCJ	NM_001042706.3	MANE Select	c.9+21408T>A		intron	N/A	NP_001036171.1
	IQCJ-SCHIP1	NM_001197113.2		c.9+21408T>A		intron	N/A	NP_001184042.1
	IQCJ-SCHIP1	NM_001197114.2		c.9+21408T>A		intron	N/A	NP_001184043.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IQCJ	ENST00000397832.7	TSL:1 MANE Select	c.9+21408T>A		intron	N/A	ENSP00000380932.2
	IQCJ-SCHIP1	ENST00000485419.7	TSL:2	c.9+21408T>A		intron	N/A	ENSP00000420182.1
	IQCJ	ENST00000451172.5	TSL:1	c.9+21408T>A		intron	N/A	ENSP00000402153.1

Frequencies

GnomAD3 genomes AF: 0.548 AC: 82975 AN: 151538 Hom.: 25880 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.586

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.547 AC: 82999 AN: 151656 Hom.: 25889 Cov.: 32 AF XY: 0.547 AC XY: 40580 AN XY: 74132

African (AFR) AF: 0.235 AC: 9656 AN: 41082

American (AMR) AF: 0.620 AC: 9464 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2357 AN: 3464

East Asian (EAS) AF: 0.471 AC: 2433 AN: 5162

South Asian (SAS) AF: 0.616 AC: 2968 AN: 4822

European-Finnish (FIN) AF: 0.697 AC: 7378 AN: 10584

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46675 AN: 67974

Other (OTH) AF: 0.585 AC: 1234 AN: 2108

Alfa AF: 0.609 Hom.: 3781

Bravo AF: 0.526

Asia WGS AF: 0.562 AC: 1955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.4
DANN	Benign	0.60
PhyloP100		0.35
Mutation Taster		=100/0	polymorphism (auto)

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: rs1472578; hg19: chr3-158808638;