chr7-93435880-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001742.4(CALCR):c.1149+72A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 596,124 control chromosomes in the GnomAD database, including 7,781 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.11 ( 1450 hom., cov: 32)
Exomes 𝑓: 0.14 ( 6331 hom. )
Consequence
CALCR
NM_001742.4 intron
NM_001742.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.526
Genes affected
CALCR (HGNC:1440): (calcitonin receptor) This gene encodes a high affinity receptor for the peptide hormone calcitonin and belongs to a subfamily of seven transmembrane-spanning G protein-coupled receptors. The encoded protein is involved in maintaining calcium homeostasis and in regulating osteoclast-mediated bone resorption. Polymorphisms in this gene have been associated with variations in bone mineral density and onset of osteoporosis. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
?
Variant 7-93435880-T-C is Benign according to our data. Variant chr7-93435880-T-C is described in ClinVar as [Benign]. Clinvar id is 1274911.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CALCR | NM_001742.4 | c.1149+72A>G | intron_variant | ENST00000426151.7 | |||
CALCR | NM_001164737.3 | c.1197+72A>G | intron_variant | ||||
CALCR | NM_001164738.2 | c.1149+72A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CALCR | ENST00000426151.7 | c.1149+72A>G | intron_variant | 1 | NM_001742.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.113 AC: 17147AN: 151802Hom.: 1453 Cov.: 32
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GnomAD4 exome AF: 0.137 AC: 60787AN: 444206Hom.: 6331 AF XY: 0.137 AC XY: 32063AN XY: 234188
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GnomAD4 genome ? AF: 0.113 AC: 17138AN: 151918Hom.: 1450 Cov.: 32 AF XY: 0.117 AC XY: 8678AN XY: 74258
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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 | GeneDx | Nov 10, 2018 | - - |
Computational scores
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Cadd
Benign
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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