3-159090849-T-A

Position:

• chr3-159090849-T-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IQCJ	NM_001042706.3	c.9+21408T>A		intron_variant		ENST00000397832.7	NP_001036171.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IQCJ	ENST00000397832.7	c.9+21408T>A		intron_variant		1	NM_001042706.3	ENSP00000380932.2
IQCJ-SCHIP1	ENST00000485419.7	c.9+21408T>A		intron_variant		2		ENSP00000420182.1

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

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.585

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.4
DANN	Benign	0.60

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

LitVar

Other links and lift over

dbSNP: rs1472578; hg19: chr3-158808638;