Variant chr7-2573408-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_152558.5(IQCE):c.395-10G>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 1,321,936 control chromosomes in the GnomAD database, including 358,586 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.75 ( 42947 hom., cov: 33)

Exomes 𝑓: 0.73 ( 315639 hom. )

Consequence

IQCE
NM_152558.5 splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.000007888

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: -0.422

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 7-2573408-G-C is Benign according to our data. Variant chr7-2573408-G-C is described in ClinVar as [Benign]. Clinvar id is 1300116.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 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.395-10G>C		splice_polypyrimidine_tract_variant, intron_variant		ENST00000402050.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IQCE	ENST00000402050.7 linkuse as main transcript	c.395-10G>C		splice_polypyrimidine_tract_variant, intron_variant		1	NM_152558.5	A2	Q6IPM2-1

Frequencies

GnomAD3 genomes

AF:

0.749

AC:

113920

AN:

152068

Hom.:

42913

Cov.:

show subpopulations

Gnomad AFR

AF:

0.771

Gnomad AMI

AF:

0.847

Gnomad AMR

AF:

0.726

Gnomad ASJ

AF:

0.688

Gnomad EAS

AF:

0.486

Gnomad SAS

AF:

0.739

Gnomad FIN

AF:

0.825

Gnomad MID

AF:

0.642

Gnomad NFE

AF:

0.753

Gnomad OTH

AF:

0.721

GnomAD3 exomes

AF:

0.733

AC:

176233

AN:

240320

Hom.:

65458

AF XY:

0.735

AC XY:

95959

AN XY:

130606

show subpopulations

Gnomad AFR exome

AF:

0.775

Gnomad AMR exome

AF:

0.725

Gnomad ASJ exome

AF:

0.697

Gnomad EAS exome

AF:

0.474

Gnomad SAS exome

AF:

0.753

Gnomad FIN exome

AF:

0.820

Gnomad NFE exome

AF:

0.752

Gnomad OTH exome

AF:

0.736

GnomAD4 exome

AF:

0.732

AC:

855877

AN:

1169750

Hom.:

315639

Cov.:

AF XY:

0.734

AC XY:

437228

AN XY:

595868

show subpopulations

Gnomad4 AFR exome

AF:

0.752

Gnomad4 AMR exome

AF:

0.722

Gnomad4 ASJ exome

AF:

0.701

Gnomad4 EAS exome

AF:

0.488

Gnomad4 SAS exome

AF:

0.752

Gnomad4 FIN exome

AF:

0.819

Gnomad4 NFE exome

AF:

0.737

Gnomad4 OTH exome

AF:

0.720

GnomAD4 genome

AF:

0.749

AC:

114014

AN:

152186

Hom.:

42947

Cov.:

AF XY:

0.750

AC XY:

55761

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.771

Gnomad4 AMR

AF:

0.726

Gnomad4 ASJ

AF:

0.688

Gnomad4 EAS

AF:

0.486

Gnomad4 SAS

AF:

0.739

Gnomad4 FIN

AF:

0.825

Gnomad4 NFE

AF:

0.753

Gnomad4 OTH

AF:

0.723

Alfa

AF:

0.745

Hom.:

13740

Bravo

AF:

0.740

Asia WGS

AF:

0.647

AC:

2254

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

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

-0.92

CADD

Benign

1.1

DANN

Benign

0.46

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0000079

dbscSNV1_RF

Benign

0.0

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