7-123488966-T-C

Position:

• chr7-123488966-T-C

Variant summary

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

The ENST00000324698.11(IQUB):​c.1234+7730A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,122 control chromosomes in the GnomAD database, including 50,101 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 0.81 (50101 hom., cov: 31)
• Consequence: IQUB ENST00000324698.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56

Genes affected

IQUB (HGNC:21995): (IQ motif and ubiquitin domain containing) Predicted to be involved in cilium assembly. Predicted to act upstream of or within smoothened signaling pathway. Predicted to be active in acrosomal vesicle and motile cilium. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IQUB	NM_178827.5	c.1234+7730A>G		intron_variant		ENST00000324698.11	NP_849149.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IQUB	ENST00000324698.11	c.1234+7730A>G		intron_variant		1	NM_178827.5	ENSP00000324882	P1
IQUB	ENST00000466202.5	c.1234+7730A>G		intron_variant		1		ENSP00000417769	P1
IQUB	ENST00000469057.1	c.1234+7730A>G		intron_variant, NMD_transcript_variant		2		ENSP00000417636
IQUB	ENST00000484508.5	c.1234+7730A>G		intron_variant, NMD_transcript_variant		2		ENSP00000417285

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123283 AN: 152004 Hom.: 50043 Cov.: 31

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.811 AC: 123399 AN: 152122 Hom.: 50101 Cov.: 31 AF XY: 0.812 AC XY: 60380 AN XY: 74366

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.826

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.863

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.805

Alfa AF: 0.806 Hom.: 44357

Bravo AF: 0.810

Asia WGS AF: 0.783 AC: 2721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.52

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: rs7791660; hg19: chr7-123129020;