Variant 3-121799150-A-G 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.766+46T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 1,457,066 control chromosomes in the GnomAD database, including 8,554 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 851 hom., cov: 31)

Exomes 𝑓: 0.11 ( 7703 hom. )

Consequence

IQCB1
NM_001023570.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.491

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 3-121799150-A-G is Benign according to our data. Variant chr3-121799150-A-G is described in ClinVar as [Benign]. Clinvar id is 257094.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IQCB1	NM_001023570.4 linkuse as main transcript	c.766+46T>C		intron_variant		ENST00000310864.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IQCB1	ENST00000310864.11 linkuse as main transcript	c.766+46T>C		intron_variant		1	NM_001023570.4	P1	Q15051-1

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15628

AN:

151582

Hom.:

851

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.0658

Gnomad AMR

AF:

0.0716

Gnomad ASJ

AF:

0.107

Gnomad EAS

AF:

0.0720

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.103

Gnomad OTH

AF:

0.104

GnomAD3 exomes

AF:

0.102

AC:

24035

AN:

235088

Hom.:

1381

AF XY:

0.107

AC XY:

13626

AN XY:

127866

show subpopulations

Gnomad AFR exome

AF:

0.109

Gnomad AMR exome

AF:

0.0488

Gnomad ASJ exome

AF:

0.104

Gnomad EAS exome

AF:

0.0606

Gnomad SAS exome

AF:

0.161

Gnomad FIN exome

AF:

0.133

Gnomad NFE exome

AF:

0.102

Gnomad OTH exome

AF:

0.110

GnomAD4 exome

AF:

0.106

AC:

137889

AN:

1305366

Hom.:

7703

Cov.:

AF XY:

0.108

AC XY:

70865

AN XY:

656666

show subpopulations

Gnomad4 AFR exome

AF:

0.103

Gnomad4 AMR exome

AF:

0.0497

Gnomad4 ASJ exome

AF:

0.109

Gnomad4 EAS exome

AF:

0.0751

Gnomad4 SAS exome

AF:

0.159

Gnomad4 FIN exome

AF:

0.135

Gnomad4 NFE exome

AF:

0.103

Gnomad4 OTH exome

AF:

0.106

GnomAD4 genome

AF:

0.103

AC:

15626

AN:

151700

Hom.:

851

Cov.:

AF XY:

0.104

AC XY:

7738

AN XY:

74154

show subpopulations

Gnomad4 AFR

AF:

0.105

Gnomad4 AMR

AF:

0.0715

Gnomad4 ASJ

AF:

0.107

Gnomad4 EAS

AF:

0.0714

Gnomad4 SAS

AF:

0.154

Gnomad4 FIN

AF:

0.133

Gnomad4 NFE

AF:

0.103

Gnomad4 OTH

AF:

0.108

Alfa

AF:

0.105

Hom.:

157

Bravo

AF:

0.0935

Asia WGS

AF:

0.135

AC:

467

AN:

3470

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 13, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

DANN

Benign

0.83

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

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