3-159025223-A-G

Variant names:

• chr3-159025223-A-G
• rs1112924
• ENST00000481796.1:n.370+61926A>G

Variant summary

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

The ENST00000639147.1(IQCJ-SCHIP1):​n.71+62918A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 152,048 control chromosomes in the GnomAD database, including 33,301 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 0.63 (33301 hom., cov: 32)
• Consequence: IQCJ-SCHIP1 ENST00000639147.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IQCJ	ENST00000481796.1	n.370+61926A>G		intron_variant	Intron 1 of 2	4		ENSP00000520496.1
IQCJ-SCHIP1	ENST00000639147.1	n.71+62918A>G		intron_variant	Intron 1 of 3	3		ENSP00000520495.1

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95850 AN: 151928 Hom.: 33296 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.631 AC: 95872 AN: 152048 Hom.: 33301 Cov.: 32 AF XY: 0.634 AC XY: 47080 AN XY: 74312

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.747

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.762

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.649

Alfa AF: 0.737 Hom.: 66937

Bravo AF: 0.620

Asia WGS AF: 0.752 AC: 2613 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1112924; hg19: chr3-158743012;