rs7102149
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004055.5(CAPN5):c.165+3126G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 1,033,198 control chromosomes in the GnomAD database, including 56,987 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 0.30 ( 7211 hom., cov: 29)
Exomes 𝑓: 0.31 ( 49776 hom. )
Consequence
CAPN5
NM_004055.5 intron
NM_004055.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.15
Genes affected
CAPN5 (HGNC:1482): (calpain 5) Calpains are calcium-dependent cysteine proteases involved in signal transduction in a variety of cellular processes. A functional calpain protein consists of an invariant small subunit and 1 of a family of large subunits. CAPN5 is one of the large subunits. Unlike some of the calpains, CAPN5 and CAPN6 lack a calmodulin-like domain IV. Because of the significant similarity to Caenorhabditis elegans sex determination gene tra-3, CAPN5 is also called as HTRA3. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAPN5 | NM_004055.5 | c.165+3126G>A | intron_variant | ENST00000648180.1 | |||
CAPN5 | XM_011545225.1 | c.285+3126G>A | intron_variant | ||||
CAPN5 | XM_017018223.3 | c.273+3126G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAPN5 | ENST00000648180.1 | c.165+3126G>A | intron_variant | NM_004055.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.297 AC: 44947AN: 151462Hom.: 7209 Cov.: 29
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GnomAD4 exome AF: 0.313 AC: 275785AN: 881618Hom.: 49776 AF XY: 0.312 AC XY: 137228AN XY: 439404
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GnomAD4 genome ? AF: 0.297 AC: 44969AN: 151580Hom.: 7211 Cov.: 29 AF XY: 0.294 AC XY: 21718AN XY: 73992
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at