Variant 7-2573428-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_152558.5(IQCE):c.405T>C(p.Pro135=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 1,467,512 control chromosomes in the GnomAD database, including 14,948 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 1747 hom., cov: 32)

Exomes 𝑓: 0.14 ( 13201 hom. )

Consequence

IQCE
NM_152558.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: -1.69

Variant links:

Genes affected

IQCE (HGNC:29171): (IQ motif containing E) Involved in limb morphogenesis. Predicted to be extrinsic component of membrane. Predicted to be part of plasma membrane protein complex. [provided by Alliance of Genome Resources, Apr 2022]

IQCE links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 7-2573428-T-C is Benign according to our data. Variant chr7-2573428-T-C is described in ClinVar as [Benign]. Clinvar id is 1300117.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.69 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IQCE	NM_152558.5 linkuse as main transcript	c.405T>C	p.Pro135=	synonymous_variant	6/22	ENST00000402050.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IQCE	ENST00000402050.7 linkuse as main transcript	c.405T>C	p.Pro135=	synonymous_variant	6/22	1	NM_152558.5	A2	Q6IPM2-1

Frequencies

GnomAD3 genomes

AF:

0.142

AC:

21602

AN:

152184

Hom.:

1747

Cov.:

show subpopulations

Gnomad AFR

AF:

0.127

Gnomad AMI

AF:

0.0758

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.0816

Gnomad EAS

AF:

0.00288

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.213

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.165

Gnomad OTH

AF:

0.120

GnomAD3 exomes

AF:

0.137

AC:

33655

AN:

245872

Hom.:

2794

AF XY:

0.138

AC XY:

18480

AN XY:

133512

show subpopulations

Gnomad AFR exome

AF:

0.126

Gnomad AMR exome

AF:

0.101

Gnomad ASJ exome

AF:

0.0831

Gnomad EAS exome

AF:

0.00134

Gnomad SAS exome

AF:

0.124

Gnomad FIN exome

AF:

0.209

Gnomad NFE exome

AF:

0.165

Gnomad OTH exome

AF:

0.134

GnomAD4 exome

AF:

0.135

AC:

178157

AN:

1315210

Hom.:

13201

Cov.:

AF XY:

0.136

AC XY:

90149

AN XY:

662118

show subpopulations

Gnomad4 AFR exome

AF:

0.120

Gnomad4 AMR exome

AF:

0.103

Gnomad4 ASJ exome

AF:

0.0776

Gnomad4 EAS exome

AF:

0.000866

Gnomad4 SAS exome

AF:

0.122

Gnomad4 FIN exome

AF:

0.209

Gnomad4 NFE exome

AF:

0.142

Gnomad4 OTH exome

AF:

0.129

GnomAD4 genome

AF:

0.142

AC:

21615

AN:

152302

Hom.:

1747

Cov.:

AF XY:

0.142

AC XY:

10593

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.127

Gnomad4 AMR

AF:

0.106

Gnomad4 ASJ

AF:

0.0816

Gnomad4 EAS

AF:

0.00289

Gnomad4 SAS

AF:

0.124

Gnomad4 FIN

AF:

0.213

Gnomad4 NFE

AF:

0.165

Gnomad4 OTH

AF:

0.119

Alfa

AF:

0.153

Hom.:

1026

Bravo

AF:

0.132

Asia WGS

AF:

0.0660

AC:

227

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

IQCE-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 02, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Polydactyly, postaxial, type a7

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

2.1

DANN

Benign

0.54

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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