Variant chr21-34669919-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_053277.3(CLIC6):c.531C>G(p.Gly177=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0012 ( 0 hom., cov: 26)

Exomes 𝑓: 0.00026 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CLIC6
NM_053277.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.96

Variant links:

Genes affected

CLIC6 (HGNC:2065): (chloride intracellular channel 6) This gene encodes a member of the chloride intracellular channel family of proteins. The gene is part of a large triplicated region found on chromosomes 1, 6, and 21. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Nov 2015]

CLIC6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 21-34669919-C-G is Benign according to our data. Variant chr21-34669919-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 715385.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.96 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLIC6	NM_053277.3 linkuse as main transcript	c.531C>G	p.Gly177=	synonymous_variant	1/6	ENST00000349499.3
CLIC6	NM_001317009.2 linkuse as main transcript	c.531C>G	p.Gly177=	synonymous_variant	1/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLIC6	ENST00000349499.3 linkuse as main transcript	c.531C>G	p.Gly177=	synonymous_variant	1/6	1	NM_053277.3	P2	Q96NY7-2
CLIC6	ENST00000360731.7 linkuse as main transcript	c.531C>G	p.Gly177=	synonymous_variant	1/7	1		A2	Q96NY7-1

Frequencies

GnomAD3 genomes

AF:

0.00121

AC:

112

AN:

92894

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00154

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.000853

Gnomad ASJ

AF:

0.00120

Gnomad EAS

AF:

0.00184

Gnomad SAS

AF:

0.00212

Gnomad FIN

AF:

0.00353

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000735

Gnomad OTH

AF:

0.000806

GnomAD3 exomes

AF:

0.00173

AC:

AN:

9848

Hom.:

AF XY:

0.00148

AC XY:

AN XY:

5420

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0103

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00143

Gnomad SAS exome

AF:

0.00144

Gnomad FIN exome

AF:

0.00336

Gnomad NFE exome

AF:

0.000179

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000259

AC:

282

AN:

1088250

Hom.:

Cov.:

AF XY:

0.000279

AC XY:

145

AN XY:

520576

show subpopulations

Gnomad4 AFR exome

AF:

0.0000934

Gnomad4 AMR exome

AF:

0.00307

Gnomad4 ASJ exome

AF:

0.000466

Gnomad4 EAS exome

AF:

0.0000973

Gnomad4 SAS exome

AF:

0.00209

Gnomad4 FIN exome

AF:

0.000650

Gnomad4 NFE exome

AF:

0.000158

Gnomad4 OTH exome

AF:

0.000118

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00124

AC:

115

AN:

92920

Hom.:

Cov.:

AF XY:

0.00138

AC XY:

AN XY:

44984

show subpopulations

Gnomad4 AFR

AF:

0.00166

Gnomad4 AMR

AF:

0.000852

Gnomad4 ASJ

AF:

0.00120

Gnomad4 EAS

AF:

0.00185

Gnomad4 SAS

AF:

0.00214

Gnomad4 FIN

AF:

0.00353

Gnomad4 NFE

AF:

0.000735

Gnomad4 OTH

AF:

0.000801

Alfa

AF:

0.00128

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

4.0

DANN

Benign

0.55

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