2-240586919-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_023083.4(CAPN10):​c.8C>T​(p.Ala3Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000705 in 1,276,538 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000071 ( 0 hom. )

Consequence

CAPN10
NM_023083.4 missense

Scores

2
8
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.924
Variant links:
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 Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.15868396).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CAPN10NM_023083.4 linkc.8C>T p.Ala3Val missense_variant 1/12 ENST00000391984.7 NP_075571.2 Q9HC96-1
CAPN10NM_023085.4 linkc.8C>T p.Ala3Val missense_variant 1/10 NP_075573.3 Q9HC96-3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CAPN10ENST00000391984.7 linkc.8C>T p.Ala3Val missense_variant 1/121 NM_023083.4 ENSP00000375844.2 Q9HC96-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000705
AC:
9
AN:
1276538
Hom.:
0
Cov.:
31
AF XY:
0.00000319
AC XY:
2
AN XY:
626574
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000253
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000380
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.0000113

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMar 31, 2024The c.8C>T (p.A3V) alteration is located in exon 1 (coding exon 1) of the CAPN10 gene. This alteration results from a C to T substitution at nucleotide position 8, causing the alanine (A) at amino acid position 3 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.18
BayesDel_addAF
Uncertain
0.11
D
BayesDel_noAF
Uncertain
-0.070
CADD
Benign
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.17
T;.;.;.;.
Eigen
Benign
-0.28
Eigen_PC
Benign
-0.32
FATHMM_MKL
Uncertain
0.85
D
LIST_S2
Benign
0.83
T;T;T;T;T
M_CAP
Uncertain
0.12
D
MetaRNN
Benign
0.16
T;T;T;T;T
MetaSVM
Uncertain
-0.032
T
MutationAssessor
Benign
1.9
L;.;L;L;L
PrimateAI
Uncertain
0.78
T
PROVEAN
Benign
-0.93
N;N;N;N;N
REVEL
Uncertain
0.29
Sift
Pathogenic
0.0
D;D;D;D;D
Sift4G
Pathogenic
0.0
D;D;D;T;D
Polyphen
0.32
B;.;D;P;D
Vest4
0.25
MutPred
0.30
Loss of catalytic residue at A3 (P = 0.0467);Loss of catalytic residue at A3 (P = 0.0467);Loss of catalytic residue at A3 (P = 0.0467);Loss of catalytic residue at A3 (P = 0.0467);Loss of catalytic residue at A3 (P = 0.0467);
MVP
0.91
MPC
0.41
ClinPred
0.19
T
GERP RS
2.5
Varity_R
0.16
gMVP
0.30

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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.

Other links and lift over

dbSNP: rs1473867213; hg19: chr2-241526336; API