Variant chr10-113709362-GAGA-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_001227.5(CASP7):c.111-11664_111-11662del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00191 in 1,497,066 control chromosomes in the GnomAD database, including 51 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0019 ( 9 hom., cov: 33)

Exomes 𝑓: 0.0019 ( 42 hom. )

Consequence

CASP7
NM_001227.5 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.43

Variant links:

Genes affected

CASP7 (HGNC:1508): (caspase 7) This gene encodes a member of the cysteine-aspartic acid protease (caspase) family. Sequential activation of caspases plays a central role in the execution-phase of cell apoptosis. Caspases exist as inactive proenzymes which undergo proteolytic processing at conserved aspartic residues to produce two subunits, large and small, that dimerize to form the active enzyme. The precursor of the encoded protein is cleaved by caspase 3 and 10, is activated upon cell death stimuli and induces apoptosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]

CASP7 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 10-113709362-GAGA-G is Benign according to our data. Variant chr10-113709362-GAGA-G is described in ClinVar as [Likely_benign]. Clinvar id is 2640853.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 282 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CASP7	NM_001227.5 linkuse as main transcript	c.111-11664_111-11662del		intron_variant		ENST00000369318.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CASP7	ENST00000369318.8 linkuse as main transcript	c.111-11664_111-11662del		intron_variant		1	NM_001227.5	P1	P55210-1

Frequencies

GnomAD3 genomes

AF:

0.00185

AC:

281

AN:

152210

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000327

Gnomad ASJ

AF:

0.0542

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00538

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000808

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00489

AC:

501

AN:

102398

Hom.:

AF XY:

0.00487

AC XY:

274

AN XY:

56278

show subpopulations

Gnomad AFR exome

AF:

0.000193

Gnomad AMR exome

AF:

0.00114

Gnomad ASJ exome

AF:

0.0497

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00583

Gnomad FIN exome

AF:

0.000234

Gnomad NFE exome

AF:

0.00136

Gnomad OTH exome

AF:

0.00479

GnomAD4 exome

AF:

0.00191

AC:

2570

AN:

1344738

Hom.:

AF XY:

0.00212

AC XY:

1406

AN XY:

662192

show subpopulations

Gnomad4 AFR exome

AF:

0.000167

Gnomad4 AMR exome

AF:

0.000724

Gnomad4 ASJ exome

AF:

0.0479

Gnomad4 EAS exome

AF:

0.0000574

Gnomad4 SAS exome

AF:

0.00620

Gnomad4 FIN exome

AF:

0.0000311

Gnomad4 NFE exome

AF:

0.000619

Gnomad4 OTH exome

AF:

0.00536

GnomAD4 genome

AF:

0.00185

AC:

282

AN:

152328

Hom.:

Cov.:

AF XY:

0.00184

AC XY:

137

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.0000241

Gnomad4 AMR

AF:

0.000327

Gnomad4 ASJ

AF:

0.0542

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00559

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000808

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00723

Hom.:

Bravo

AF:

0.00176

Asia WGS

AF:

0.00173

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2023

CASP7: PM4:Supporting, BS1 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over