dbSNP rs3842570: CAPN10:c.997+136_998-148delCGGGAGGAGGGTGATGATTCTGTCCCAGGAGC (chr2-240594824-AGATGATTCTGTCCCAGGAGCCGGGAGGAGGGT-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_023083.4(CAPN10):c.997+136_998-148delCGGGAGGAGGGTGATGATTCTGTCCCAGGAGC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000909 in 660,420 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 37)

Exomes 𝑓: 0.0000091 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CAPN10
NM_023083.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.158

Publications

26 publications found

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]

CAPN10 Gene-Disease associations (from GenCC):

neurodevelopmental disorder
Inheritance: AR Classification: LIMITED Submitted by: G2P

CAPN10 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAPN10	NM_023083.4 link	c.997+136_998-148delCGGGAGGAGGGTGATGATTCTGTCCCAGGAGC		intron_variant	Intron 6 of 11	ENST00000391984.7	NP_075571.2	Q9HC96-1
CAPN10	NM_023085.4 link	c.997+136_998-148delCGGGAGGAGGGTGATGATTCTGTCCCAGGAGC		intron_variant	Intron 6 of 9		NP_075573.3	Q9HC96-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAPN10	ENST00000391984.7 link	c.997+116_997+147delGATGATTCTGTCCCAGGAGCCGGGAGGAGGGT		intron_variant	Intron 6 of 11	1	NM_023083.4	ENSP00000375844.2		Q9HC96-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

135030

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000909

AC:

AN:

660420

Hom.:

AF XY:

0.0000119

AC XY:

AN XY:

337152

show subpopulations

African (AFR)

AF:

0.000241

AC:

AN:

20758

American (AMR)

AF:

0.00

AC:

AN:

22902

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15100

East Asian (EAS)

AF:

0.00

AC:

AN:

32202

South Asian (SAS)

AF:

0.00

AC:

AN:

51992

European-Finnish (FIN)

AF:

0.00

AC:

AN:

33074

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2480

European-Non Finnish (NFE)

AF:

0.00000223

AC:

AN:

449192

Other (OTH)

AF:

0.00

AC:

AN:

32720

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

135030

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

64926

African (AFR)

AF:

0.00

AC:

AN:

37210

American (AMR)

AF:

0.00

AC:

AN:

13344

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3214

East Asian (EAS)

AF:

0.00

AC:

AN:

4368

South Asian (SAS)

AF:

0.00

AC:

AN:

3868

European-Finnish (FIN)

AF:

0.00

AC:

AN:

8568

Middle Eastern (MID)

AF:

0.00

AC:

AN:

284

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

61584

Other (OTH)

AF:

0.00

AC:

AN:

1792

Alfa

AF:

0.0000660

Hom.:

878

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.16

Mutation Taster

=98/2

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over