rs7907519

Variant names:

• chr10-113681924-A-C
• rs7907519
• NM_001227.5:c.-1+1946A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-113681924-A-C
• chr10-113681924-A-G
• chr10-113681924-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001227.5(CASP7):​c.-1+1946A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,036 control chromosomes in the GnomAD database, including 36,344 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.68 (36344 hom., cov: 31)
• Consequence: CASP7 NM_001227.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 10 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001227.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASP7	NM_001227.5	MANE Select	c.-1+1946A>C		intron	N/A	NP_001218.1	P55210-1
	CASP7	NM_001267057.1		c.224+1946A>C		intron	N/A	NP_001253986.1	P55210
	CASP7	NM_033338.6		c.-9+1946A>C		intron	N/A	NP_203124.1	P55210-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASP7	ENST00000369318.8	TSL:1 MANE Select	c.-1+1946A>C		intron	N/A	ENSP00000358324.4	P55210-1
	CASP7	ENST00000345633.8	TSL:1	c.-75+1946A>C		intron	N/A	ENSP00000298701.7	P55210-1
	CASP7	ENST00000369315.5	TSL:1	c.-108+1946A>C		intron	N/A	ENSP00000358321.1	P55210-1

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103154 AN: 151918 Hom.: 36288 Cov.: 31

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.702

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.679 AC: 103266 AN: 152036 Hom.: 36344 Cov.: 31 AF XY: 0.673 AC XY: 50026 AN XY: 74322

African (AFR) AF: 0.862 AC: 35762 AN: 41486

American (AMR) AF: 0.579 AC: 8840 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2364 AN: 3470

East Asian (EAS) AF: 0.764 AC: 3946 AN: 5166

South Asian (SAS) AF: 0.651 AC: 3126 AN: 4802

European-Finnish (FIN) AF: 0.550 AC: 5800 AN: 10552

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41130 AN: 67968

Other (OTH) AF: 0.704 AC: 1487 AN: 2112

Alfa AF: 0.616 Hom.: 2687

Bravo AF: 0.687

Asia WGS AF: 0.712 AC: 2475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.18
DANN	Benign	0.41
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7907519; hg19: chr10-115441683;