rs2235579

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001287.6(CLCN7):c.1170A>T(p.Ala390=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 1,612,790 control chromosomes in the GnomAD database, including 214,127 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.52 ( 20872 hom., cov: 35)

Exomes 𝑓: 0.51 ( 193255 hom. )

Consequence

CLCN7
NM_001287.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: -2.59

Variant links:

Genes affected

CLCN7 (HGNC:2025): (chloride voltage-gated channel 7) The product of this gene belongs to the CLC chloride channel family of proteins. Chloride channels play important roles in the plasma membrane and in intracellular organelles. This gene encodes chloride channel 7. Defects in this gene are the cause of osteopetrosis autosomal recessive type 4 (OPTB4), also called infantile malignant osteopetrosis type 2 as well as the cause of autosomal dominant osteopetrosis type 2 (OPTA2), also called autosomal dominant Albers-Schonberg disease or marble disease autosoml dominant. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. OPTA2 is the most common form of osteopetrosis, occurring in adolescence or adulthood. [provided by RefSeq, Jul 2008]

CLCN7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

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

BP6

Variant 16-1453878-T-A is Benign according to our data. Variant chr16-1453878-T-A is described in ClinVar as [Benign]. Clinvar id is 257949.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-1453878-T-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-2.59 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
CLCN7	NM_001287.6 linkuse as main transcript	c.1170A>T	p.Ala390=	synonymous_variant	14/25	ENST00000382745.9
CLCN7	NM_001114331.3 linkuse as main transcript	c.1098A>T	p.Ala366=	synonymous_variant	13/24
CLCN7	XM_011522354.2 linkuse as main transcript	c.996A>T	p.Ala332=	synonymous_variant	14/25

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLCN7	ENST00000382745.9 linkuse as main transcript	c.1170A>T	p.Ala390=	synonymous_variant	14/25	1	NM_001287.6	P1	P51798-1

Frequencies

GnomAD3 genomes

AF:

0.520

AC:

79105

AN:

152094

Hom.:

20843

Cov.:

show subpopulations

Gnomad AFR

AF:

0.518

Gnomad AMI

AF:

0.700

Gnomad AMR

AF:

0.534

Gnomad ASJ

AF:

0.520

Gnomad EAS

AF:

0.689

Gnomad SAS

AF:

0.560

Gnomad FIN

AF:

0.548

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.495

Gnomad OTH

AF:

0.519

GnomAD3 exomes

AF:

0.534

AC:

133950

AN:

250664

Hom.:

36074

AF XY:

0.531

AC XY:

72160

AN XY:

135772

show subpopulations

Gnomad AFR exome

AF:

0.522

Gnomad AMR exome

AF:

0.572

Gnomad ASJ exome

AF:

0.498

Gnomad EAS exome

AF:

0.665

Gnomad SAS exome

AF:

0.542

Gnomad FIN exome

AF:

0.547

Gnomad NFE exome

AF:

0.502

Gnomad OTH exome

AF:

0.530

GnomAD4 exome

AF:

0.512

AC:

748269

AN:

1460578

Hom.:

193255

Cov.:

AF XY:

0.513

AC XY:

372661

AN XY:

726598

show subpopulations

Gnomad4 AFR exome

AF:

0.520

Gnomad4 AMR exome

AF:

0.563

Gnomad4 ASJ exome

AF:

0.502

Gnomad4 EAS exome

AF:

0.702

Gnomad4 SAS exome

AF:

0.541

Gnomad4 FIN exome

AF:

0.551

Gnomad4 NFE exome

AF:

0.498

Gnomad4 OTH exome

AF:

0.527

GnomAD4 genome

AF:

0.520

AC:

79180

AN:

152212

Hom.:

20872

Cov.:

AF XY:

0.523

AC XY:

38930

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.519

Gnomad4 AMR

AF:

0.535

Gnomad4 ASJ

AF:

0.520

Gnomad4 EAS

AF:

0.689

Gnomad4 SAS

AF:

0.562

Gnomad4 FIN

AF:

0.548

Gnomad4 NFE

AF:

0.495

Gnomad4 OTH

AF:

0.517

Alfa

AF:

0.467

Hom.:

4978

Bravo

AF:

0.524

Asia WGS

AF:

0.621

AC:

2155

AN:

3478

EpiCase

AF:

0.507

EpiControl

AF:

0.506

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -

Hypopigmentation, organomegaly, and delayed myelination and development

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Autosomal recessive osteopetrosis 4

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Autosomal dominant osteopetrosis 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Osteopetrosis

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

Cadd

Benign

0.36

Dann

Benign

0.82

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.7

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