NM_001742.4:c.1270C>G
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001742.4(CALCR):c.1270C>G(p.Arg424Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000465 in 1,613,612 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001742.4 missense
Scores
Clinical Significance
Conservation
Publications
- osteoporosisInheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CALCR | NM_001742.4 | c.1270C>G | p.Arg424Gly | missense_variant | Exon 14 of 14 | ENST00000426151.7 | NP_001733.1 | |
CALCR | NM_001164737.3 | c.1318C>G | p.Arg440Gly | missense_variant | Exon 16 of 16 | NP_001158209.2 | ||
CALCR | NM_001164738.2 | c.1270C>G | p.Arg424Gly | missense_variant | Exon 13 of 13 | NP_001158210.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152136Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000199 AC: 5AN: 251314 AF XY: 0.0000368 show subpopulations
GnomAD4 exome AF: 0.0000499 AC: 73AN: 1461476Hom.: 0 Cov.: 31 AF XY: 0.0000426 AC XY: 31AN XY: 727064 show subpopulations
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74298 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1270C>G (p.R424G) alteration is located in exon 14 (coding exon 12) of the CALCR gene. This alteration results from a C to G substitution at nucleotide position 1270, causing the arginine (R) at amino acid position 424 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at