chr1-223712873-C-CCACGGTAGGAAGCG
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001748.5(CAPN2):c.235_237+11dup variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00753 in 1,531,350 control chromosomes in the GnomAD database, including 64 homozygotes. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.0057 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0077 ( 60 hom. )
Consequence
CAPN2
NM_001748.5 frameshift
NM_001748.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.735
Genes affected
CAPN2 (HGNC:1479): (calpain 2) The calpains, calcium-activated neutral proteases, are nonlysosomal, intracellular cysteine proteases. The mammalian calpains include ubiquitous, stomach-specific, and muscle-specific proteins. The ubiquitous enzymes consist of heterodimers with distinct large, catalytic subunits associated with a common small, regulatory subunit. This gene encodes the large subunit of the ubiquitous enzyme, calpain 2. Multiple heterogeneous transcriptional start sites in the 5' UTR have been reported. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 1-223712873-C-CCACGGTAGGAAGCG is Benign according to our data. Variant chr1-223712873-C-CCACGGTAGGAAGCG is described in ClinVar as [Benign]. Clinvar id is 790811.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAPN2 | NM_001748.5 | c.235_237+11dup | frameshift_variant | 1/21 | ENST00000295006.6 | ||
CAPN2 | XM_047431344.1 | c.235_237+11dup | frameshift_variant | 1/12 | |||
CAPN2 | NM_001146068.2 | c.4-4887_4-4874dup | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAPN2 | ENST00000295006.6 | c.235_237+11dup | frameshift_variant | 1/21 | 1 | NM_001748.5 | P1 | ||
CAPN2 | ENST00000433674.6 | c.4-4887_4-4874dup | intron_variant | 2 | |||||
CAPN2 | ENST00000434648.5 | c.4-4887_4-4874dup | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00575 AC: 874AN: 151914Hom.: 4 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
874
AN:
151914
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00533 AC: 795AN: 149096Hom.: 6 AF XY: 0.00524 AC XY: 435AN XY: 83032
GnomAD3 exomes
AF:
AC:
795
AN:
149096
Hom.:
AF XY:
AC XY:
435
AN XY:
83032
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00773 AC: 10663AN: 1379326Hom.: 60 Cov.: 34 AF XY: 0.00756 AC XY: 5164AN XY: 682966
GnomAD4 exome
AF:
AC:
10663
AN:
1379326
Hom.:
Cov.:
34
AF XY:
AC XY:
5164
AN XY:
682966
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00575 AC: 874AN: 152024Hom.: 4 Cov.: 32 AF XY: 0.00636 AC XY: 473AN XY: 74320
GnomAD4 genome
?
AF:
AC:
874
AN:
152024
Hom.:
Cov.:
32
AF XY:
AC XY:
473
AN XY:
74320
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
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 | Invitae | Aug 17, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at