Variant chr7-2572244-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.312T>C(p.Thr104=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 1,613,770 control chromosomes in the GnomAD database, including 452,641 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.71 ( 38908 hom., cov: 33)

Exomes 𝑓: 0.75 ( 413733 hom. )

Consequence

IQCE
NM_152558.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.220

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=-0.78).

BP6

Variant 7-2572244-T-C is Benign according to our data. Variant chr7-2572244-T-C is described in ClinVar as [Benign]. Clinvar id is 1300115.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.22 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.752 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.312T>C	p.Thr104=	synonymous_variant	5/22	ENST00000402050.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IQCE	ENST00000402050.7 linkuse as main transcript	c.312T>C	p.Thr104=	synonymous_variant	5/22	1	NM_152558.5	A2	Q6IPM2-1

Frequencies

GnomAD3 genomes

AF:

0.711

AC:

108125

AN:

152000

Hom.:

38877

Cov.:

show subpopulations

Gnomad AFR

AF:

0.634

Gnomad AMI

AF:

0.662

Gnomad AMR

AF:

0.712

Gnomad ASJ

AF:

0.688

Gnomad EAS

AF:

0.507

Gnomad SAS

AF:

0.743

Gnomad FIN

AF:

0.825

Gnomad MID

AF:

0.611

Gnomad NFE

AF:

0.757

Gnomad OTH

AF:

0.692

GnomAD3 exomes

AF:

0.729

AC:

181799

AN:

249464

Hom.:

67080

AF XY:

0.732

AC XY:

99140

AN XY:

135358

show subpopulations

Gnomad AFR exome

AF:

0.635

Gnomad AMR exome

AF:

0.723

Gnomad ASJ exome

AF:

0.700

Gnomad EAS exome

AF:

0.498

Gnomad SAS exome

AF:

0.760

Gnomad FIN exome

AF:

0.820

Gnomad NFE exome

AF:

0.757

Gnomad OTH exome

AF:

0.734

GnomAD4 exome

AF:

0.750

AC:

1096380

AN:

1461652

Hom.:

413733

Cov.:

AF XY:

0.751

AC XY:

546059

AN XY:

727130

show subpopulations

Gnomad4 AFR exome

AF:

0.627

Gnomad4 AMR exome

AF:

0.718

Gnomad4 ASJ exome

AF:

0.707

Gnomad4 EAS exome

AF:

0.503

Gnomad4 SAS exome

AF:

0.761

Gnomad4 FIN exome

AF:

0.819

Gnomad4 NFE exome

AF:

0.762

Gnomad4 OTH exome

AF:

0.729

GnomAD4 genome

AF:

0.711

AC:

108217

AN:

152118

Hom.:

38908

Cov.:

AF XY:

0.714

AC XY:

53070

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.634

Gnomad4 AMR

AF:

0.712

Gnomad4 ASJ

AF:

0.688

Gnomad4 EAS

AF:

0.507

Gnomad4 SAS

AF:

0.743

Gnomad4 FIN

AF:

0.825

Gnomad4 NFE

AF:

0.757

Gnomad4 OTH

AF:

0.694

Alfa

AF:

0.728

Hom.:

10540

Bravo

AF:

0.697

Asia WGS

AF:

0.645

AC:

2248

AN:

3478

EpiCase

AF:

0.747

EpiControl

AF:

0.741

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

Feb 01, 2023

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

-0.78

CADD

Benign

5.7

DANN

Benign

0.53

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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