Variant rs3749166 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_023083.4(CAPN10):c.1860G>A(p.Ala620Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 1,612,786 control chromosomes in the GnomAD database, including 287,257 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.52 ( 22198 hom., cov: 33)

Exomes 𝑓: 0.60 ( 265059 hom. )

Consequence

CAPN10
NM_023083.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.29

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 links:

CAPN10 (HGNC:):

CAPN10 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 2-240598004-G-A is Benign according to our data. Variant chr2-240598004-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAPN10	NM_023083.4 linkuse as main transcript	c.1860G>A	p.Ala620Ala	synonymous_variant	10/12	ENST00000391984.7	NP_075571.2	Q9HC96-1
CAPN10	NM_023085.4 linkuse as main transcript	c.1395G>A	p.Ala465Ala	synonymous_variant	8/10		NP_075573.3	Q9HC96-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAPN10	ENST00000391984.7 linkuse as main transcript	c.1860G>A	p.Ala620Ala	synonymous_variant	10/12	1	NM_023083.4	ENSP00000375844.2		Q9HC96-1

Frequencies

GnomAD3 genomes

AF:

0.524

AC:

79636

AN:

151872

Hom.:

22182

Cov.:

show subpopulations

Gnomad AFR

AF:

0.320

Gnomad AMI

AF:

0.721

Gnomad AMR

AF:

0.577

Gnomad ASJ

AF:

0.606

Gnomad EAS

AF:

0.657

Gnomad SAS

AF:

0.566

Gnomad FIN

AF:

0.551

Gnomad MID

AF:

0.554

Gnomad NFE

AF:

0.612

Gnomad OTH

AF:

0.554

GnomAD3 exomes

AF:

0.583

AC:

145961

AN:

250162

Hom.:

43461

AF XY:

0.589

AC XY:

79794

AN XY:

135580

show subpopulations

Gnomad AFR exome

AF:

0.309

Gnomad AMR exome

AF:

0.606

Gnomad ASJ exome

AF:

0.600

Gnomad EAS exome

AF:

0.659

Gnomad SAS exome

AF:

0.569

Gnomad FIN exome

AF:

0.542

Gnomad NFE exome

AF:

0.613

Gnomad OTH exome

AF:

0.589

GnomAD4 exome

AF:

0.600

AC:

875966

AN:

1460796

Hom.:

265059

Cov.:

AF XY:

0.600

AC XY:

436128

AN XY:

726736

show subpopulations

Gnomad4 AFR exome

AF:

0.300

Gnomad4 AMR exome

AF:

0.604

Gnomad4 ASJ exome

AF:

0.596

Gnomad4 EAS exome

AF:

0.645

Gnomad4 SAS exome

AF:

0.573

Gnomad4 FIN exome

AF:

0.552

Gnomad4 NFE exome

AF:

0.612

Gnomad4 OTH exome

AF:

0.593

GnomAD4 genome

AF:

0.524

AC:

79684

AN:

151990

Hom.:

22198

Cov.:

AF XY:

0.524

AC XY:

38953

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.320

Gnomad4 AMR

AF:

0.577

Gnomad4 ASJ

AF:

0.606

Gnomad4 EAS

AF:

0.658

Gnomad4 SAS

AF:

0.566

Gnomad4 FIN

AF:

0.551

Gnomad4 NFE

AF:

0.612

Gnomad4 OTH

AF:

0.556

Alfa

AF:

0.577

Hom.:

16356

Bravo

AF:

0.518

Asia WGS

AF:

0.594

AC:

2062

AN:

3478

EpiCase

AF:

0.602

EpiControl

AF:

0.601

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

7.6

DANN

Benign

0.58

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.44

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.44

Position offset: 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

Computational scores

Splicing

Publications

LitVar

Other links and lift over