Variant rs1920320 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001023570.4(IQCB1):c.101-48T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 1,325,464 control chromosomes in the GnomAD database, including 47,486 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 4959 hom., cov: 32)

Exomes 𝑓: 0.26 ( 42527 hom. )

Consequence

IQCB1
NM_001023570.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.66

Variant links:

Genes affected

IQCB1 (HGNC:28949): (IQ motif containing B1) This gene encodes a nephrocystin protein that interacts with calmodulin and the retinitis pigmentosa GTPase regulator protein. The encoded protein has a central coiled-coil region and two calmodulin-binding IQ domains. It is localized to the primary cilia of renal epithelial cells and connecting cilia of photoreceptor cells. The protein is thought to play a role in ciliary function. Defects in this gene result in Senior-Loken syndrome type 5. Alternative splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 6. [provided by RefSeq, Jan 2016]

IQCB1 links:

IQCB1 (HGNC:):

IQCB1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 3-121828680-A-G is Benign according to our data. Variant chr3-121828680-A-G is described in ClinVar as [Benign]. Clinvar id is 257089.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IQCB1	NM_001023570.4 linkuse as main transcript	c.101-48T>C		intron_variant		ENST00000310864.11	NP_001018864.2	Q15051-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IQCB1	ENST00000310864.11 linkuse as main transcript	c.101-48T>C		intron_variant		1	NM_001023570.4	ENSP00000311505.6		Q15051-1

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37465

AN:

151996

Hom.:

4958

Cov.:

show subpopulations

Gnomad AFR

AF:

0.256

Gnomad AMI

AF:

0.396

Gnomad AMR

AF:

0.151

Gnomad ASJ

AF:

0.222

Gnomad EAS

AF:

0.0799

Gnomad SAS

AF:

0.0981

Gnomad FIN

AF:

0.281

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.229

GnomAD3 exomes

AF:

0.218

AC:

45803

AN:

209938

Hom.:

5680

AF XY:

0.216

AC XY:

24584

AN XY:

113926

show subpopulations

Gnomad AFR exome

AF:

0.258

Gnomad AMR exome

AF:

0.123

Gnomad ASJ exome

AF:

0.219

Gnomad EAS exome

AF:

0.0810

Gnomad SAS exome

AF:

0.108

Gnomad FIN exome

AF:

0.288

Gnomad NFE exome

AF:

0.285

Gnomad OTH exome

AF:

0.220

GnomAD4 exome

AF:

0.260

AC:

305469

AN:

1173350

Hom.:

42527

Cov.:

AF XY:

0.254

AC XY:

151222

AN XY:

594562

show subpopulations

Gnomad4 AFR exome

AF:

0.260

Gnomad4 AMR exome

AF:

0.129

Gnomad4 ASJ exome

AF:

0.215

Gnomad4 EAS exome

AF:

0.0891

Gnomad4 SAS exome

AF:

0.110

Gnomad4 FIN exome

AF:

0.284

Gnomad4 NFE exome

AF:

0.289

Gnomad4 OTH exome

AF:

0.239

GnomAD4 genome

AF:

0.246

AC:

37476

AN:

152114

Hom.:

4959

Cov.:

AF XY:

0.239

AC XY:

17744

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.255

Gnomad4 AMR

AF:

0.150

Gnomad4 ASJ

AF:

0.222

Gnomad4 EAS

AF:

0.0799

Gnomad4 SAS

AF:

0.0981

Gnomad4 FIN

AF:

0.281

Gnomad4 NFE

AF:

0.280

Gnomad4 OTH

AF:

0.228

Alfa

AF:

0.248

Hom.:

894

Bravo

AF:

0.242

Asia WGS

AF:

0.116

AC:

408

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over