3-159138307-T-G

Variant names:

• chr3-159138307-T-G
• rs1501288
• NM_001042706.3:c.9+68866T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001042706.3(IQCJ):​c.9+68866T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 152,012 control chromosomes in the GnomAD database, including 35,054 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 0.68 (35054 hom., cov: 32)
• Consequence: IQCJ NM_001042706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IQCJ	NM_001042706.3	c.9+68866T>G		intron_variant	Intron 1 of 3	ENST00000397832.7	NP_001036171.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IQCJ	ENST00000397832.7	c.9+68866T>G		intron_variant	Intron 1 of 3	1	NM_001042706.3	ENSP00000380932.2
IQCJ-SCHIP1	ENST00000485419.7	c.9+68866T>G		intron_variant	Intron 1 of 10	2		ENSP00000420182.1

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102996 AN: 151894 Hom.: 35034 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.678 AC: 103068 AN: 152012 Hom.: 35054 Cov.: 32 AF XY: 0.673 AC XY: 49980 AN XY: 74298

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.690

Alfa AF: 0.695 Hom.: 7440

Bravo AF: 0.677

Asia WGS AF: 0.684 AC: 2379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.8
DANN	Benign	0.79

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: rs1501288; hg19: chr3-158856096;