3-159025223-A-G

Variant names:

• chr3-159025223-A-G
• rs1112924
• ENST00000639147.2:c.-172+62918A>G

Variant summary

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

The ENST00000639147.2(IQCJ-SCHIP1):​c.-172+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 ENST00000639147.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 1 publications found

Genes affected

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]

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000639147.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IQCJ-SCHIP1	ENST00000639147.2	TSL:3	c.-172+62918A>G		intron	N/A	ENSP00000520495.1
	IQCJ	ENST00000481796.2	TSL:4	c.-172+61926A>G		intron	N/A	ENSP00000520496.1

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

African (AFR) AF: 0.311 AC: 12913 AN: 41466

American (AMR) AF: 0.747 AC: 11404 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2481 AN: 3472

East Asian (EAS) AF: 0.874 AC: 4525 AN: 5180

South Asian (SAS) AF: 0.762 AC: 3672 AN: 4820

European-Finnish (FIN) AF: 0.706 AC: 7458 AN: 10562

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51038 AN: 67960

Other (OTH) AF: 0.649 AC: 1368 AN: 2108

Alfa AF: 0.707 Hom.: 106433

Bravo AF: 0.620

Asia WGS AF: 0.752 AC: 2613 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.47
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1112924; hg19: chr3-158743012;