rs2975760
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_023083.4(CAPN10):c.471-187T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 605,384 control chromosomes in the GnomAD database, including 7,381 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).
Frequency
Genomes: 𝑓 0.13 ( 1455 hom., cov: 34)
Exomes 𝑓: 0.16 ( 5926 hom. )
Consequence
CAPN10
NM_023083.4 intron
NM_023083.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.31
Genes affected
CAPN10 (HGNC:1477): (calpain 10) Calpains represent a 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 catalytic subunit has four domains: domain I, the N-terminal regulatory domain that is processed upon calpain activation; domain II, the protease domain; domain III, a linker domain of unknown function; and domain IV, the calmodulin-like calcium-binding domain. This gene encodes a large subunit. It is an atypical calpain in that it lacks the calmodulin-like calcium-binding domain and instead has a divergent C-terminal domain. It is similar in organization to calpains 5 and 6. This gene is associated with type 2 or non-insulin-dependent diabetes mellitus (NIDDM), and is located within the NIDDM1 region. Multiple alternative transcript variants have been described for this gene. [provided by RefSeq, Sep 2010]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAPN10 | NM_023083.4 | c.471-187T>C | intron_variant | ENST00000391984.7 | |||
CAPN10 | NM_023085.4 | c.471-187T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAPN10 | ENST00000391984.7 | c.471-187T>C | intron_variant | 1 | NM_023083.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.126 AC: 19152AN: 152150Hom.: 1454 Cov.: 34
GnomAD3 genomes
?
AF:
AC:
19152
AN:
152150
Hom.:
Cov.:
34
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:
GnomAD4 exome AF: 0.156 AC: 70693AN: 453116Hom.: 5926 Cov.: 5 AF XY: 0.157 AC XY: 37330AN XY: 237166
GnomAD4 exome
AF:
AC:
70693
AN:
453116
Hom.:
Cov.:
5
AF XY:
AC XY:
37330
AN XY:
237166
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: 0.126 AC: 19162AN: 152268Hom.: 1455 Cov.: 34 AF XY: 0.127 AC XY: 9460AN XY: 74432
GnomAD4 genome
?
AF:
AC:
19162
AN:
152268
Hom.:
Cov.:
34
AF XY:
AC XY:
9460
AN XY:
74432
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.:
Bravo
AF:
Asia WGS
AF:
AC:
513
AN:
3478
ClinVar
Significance: risk factor
Submissions summary: Other:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
POLYCYSTIC OVARY SYNDROME, SUSCEPTIBILITY TO Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Nov 01, 2003 | - - |
Type 2 diabetes mellitus 1, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Nov 01, 2003 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at