chr11-65182860-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_005186.4(CAPN1):c.159G>A(p.Gly53=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00121 in 1,601,476 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0056 ( 10 hom., cov: 32)
Exomes 𝑓: 0.00074 ( 13 hom. )
Consequence
CAPN1
NM_005186.4 synonymous
NM_005186.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.121
Genes affected
CAPN1 (HGNC:1476): (calpain 1) The calpains, calcium-activated neutral proteases, are nonlysosomal, intracellular cysteine proteases. The mammalian calpains include ubiquitous, stomach-specific, and muscle-specific proteins. The ubiquitous enzymes consist of heterodimers with distinct large, catalytic subunits associated with a common small, regulatory subunit. This gene encodes the large subunit of the ubiquitous enzyme, calpain 1. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
?
Variant 11-65182860-G-A is Benign according to our data. Variant chr11-65182860-G-A is described in ClinVar as [Benign]. Clinvar id is 720350.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-65182860-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.121 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00562 (856/152234) while in subpopulation AFR AF= 0.0186 (772/41526). AF 95% confidence interval is 0.0175. There are 10 homozygotes in gnomad4. There are 414 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAPN1 | NM_005186.4 | c.159G>A | p.Gly53= | synonymous_variant | 2/22 | ENST00000279247.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAPN1 | ENST00000279247.11 | c.159G>A | p.Gly53= | synonymous_variant | 2/22 | 1 | NM_005186.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00557 AC: 847AN: 152116Hom.: 9 Cov.: 32
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GnomAD3 exomes AF: 0.00134 AC: 302AN: 225896Hom.: 2 AF XY: 0.00104 AC XY: 127AN XY: 122524
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GnomAD4 exome AF: 0.000742 AC: 1075AN: 1449242Hom.: 13 Cov.: 31 AF XY: 0.000671 AC XY: 483AN XY: 719892
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at