Variant chrX-111251300-GA-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_014289.4(CAPN6):c.894-15delT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0046 ( 1 hom., 64 hem., cov: 18)

Exomes 𝑓: 0.078 ( 0 hom. 101 hem. )

Consequence

CAPN6
NM_014289.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.31

Variant links:

Genes affected

CAPN6 (HGNC:1483): (calpain 6) Calpains are ubiquitous, well-conserved family of calcium-dependent, cysteine proteases. The calpain proteins are heterodimers consisting of an invariant small subunit and variable large subunits. The large subunit possesses a cysteine protease domain, and both subunits possess calcium-binding domains. Calpains have been implicated in neurodegenerative processes, as their activation can be triggered by calcium influx and oxidative stress. The protein encoded by this gene is highly expressed in the placenta. Its C-terminal region lacks any homology to the calmodulin-like domain of other calpains. The protein lacks critical active site residues and thus is suggested to be proteolytically inactive. The protein may play a role in tumor formation by inhibiting apoptosis and promoting angiogenesis. [provided by RefSeq, Nov 2009]

CAPN6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant X-111251300-GA-G is Benign according to our data. Variant chrX-111251300-GA-G is described in ClinVar as [Benign]. Clinvar id is 1221767.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAPN6	NM_014289.4 linkuse as main transcript	c.894-15delT		intron_variant		ENST00000324068.2	NP_055104.2	Q9Y6Q1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAPN6	ENST00000324068.2 linkuse as main transcript	c.894-15delT		intron_variant		1	NM_014289.4	ENSP00000317214.1		Q9Y6Q1

Frequencies

GnomAD3 genomes

AF:

0.00458

AC:

392

AN:

85631

Hom.:

Cov.:

AF XY:

0.00314

AC XY:

AN XY:

20353

show subpopulations

Gnomad AFR

AF:

0.00822

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00287

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00872

Gnomad SAS

AF:

0.00636

Gnomad FIN

AF:

0.00559

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00270

Gnomad OTH

AF:

0.000891

GnomAD3 exomes

AF:

0.188

AC:

8508

AN:

45184

Hom.:

AF XY:

0.00637

AC XY:

AN XY:

2042

show subpopulations

Gnomad AFR exome

AF:

0.0630

Gnomad AMR exome

AF:

0.188

Gnomad ASJ exome

AF:

0.219

Gnomad EAS exome

AF:

0.212

Gnomad SAS exome

AF:

0.206

Gnomad FIN exome

AF:

0.177

Gnomad NFE exome

AF:

0.214

Gnomad OTH exome

AF:

0.204

GnomAD4 exome

AF:

0.0777

AC:

51293

AN:

660164

Hom.:

Cov.:

AF XY:

0.000599

AC XY:

101

AN XY:

168656

show subpopulations

Gnomad4 AFR exome

AF:

0.0263

Gnomad4 AMR exome

AF:

0.0926

Gnomad4 ASJ exome

AF:

0.0825

Gnomad4 EAS exome

AF:

0.0807

Gnomad4 SAS exome

AF:

0.0626

Gnomad4 FIN exome

AF:

0.0787

Gnomad4 NFE exome

AF:

0.0798

Gnomad4 OTH exome

AF:

0.0768

GnomAD4 genome

AF:

0.00458

AC:

392

AN:

85628

Hom.:

Cov.:

AF XY:

0.00314

AC XY:

AN XY:

20364

show subpopulations

Gnomad4 AFR

AF:

0.00821

Gnomad4 AMR

AF:

0.00274

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00913

Gnomad4 SAS

AF:

0.00641

Gnomad4 FIN

AF:

0.00559

Gnomad4 NFE

AF:

0.00270

Gnomad4 OTH

AF:

0.000881

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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