rs1472578

chr3-159090849-T-Achr3-159090849-T-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+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:):

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	UniProt
IQCJ	NM_001042706.3	c.9+21408T>A		intron_variant		ENST00000397832.7
IQCJ-SCHIP1	NM_001197113.2	c.9+21408T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IQCJ	ENST00000397832.7	c.9+21408T>A		intron_variant		1	NM_001042706.3
IQCJ	ENST00000451172.5	c.9+21408T>A		intron_variant		1		P1
IQCJ	ENST00000482126.1	c.9+21408T>A		intron_variant		1
IQCJ	ENST00000481796.1	n.370+127552T>A		intron_variant, non_coding_transcript_variant		4

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;