NM_001742.4:c.1358delA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001742.4(CALCR):βc.1358delAβ(p.Asn453ThrfsTer13) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000379 in 1,613,934 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (β β ).
Frequency
Consequence
NM_001742.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CALCR | NM_001742.4 | c.1358delA | p.Asn453ThrfsTer13 | frameshift_variant | Exon 14 of 14 | ENST00000426151.7 | NP_001733.1 | |
CALCR | NM_001164737.3 | c.1406delA | p.Asn469ThrfsTer13 | frameshift_variant | Exon 16 of 16 | NP_001158209.2 | ||
CALCR | NM_001164738.2 | c.1358delA | p.Asn453ThrfsTer13 | frameshift_variant | Exon 13 of 13 | NP_001158210.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000223 AC: 34AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000207 AC: 52AN: 251494Hom.: 0 AF XY: 0.000206 AC XY: 28AN XY: 135922
GnomAD4 exome AF: 0.000395 AC: 577AN: 1461666Hom.: 0 Cov.: 30 AF XY: 0.000397 AC XY: 289AN XY: 727152
GnomAD4 genome AF: 0.000223 AC: 34AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: CALCR c.1358delA (p.Asn453ThrfsX13) results in a premature termination codon, predicted to cause a truncation of the encoded protein. However, clinical and functional evidence currently available does not allow for definitive conclusions on whether loss-of-function variants in the CALCR gene cause disease. The variant allele was found at a frequency of 0.00021 in 251494 control chromosomes (52/251494 chromosomes from the gnomAD database). To our knowledge, no occurrence of c.1358delA in individuals affected with Postmenopausal Osteoporosis and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance. -
not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at