3-122254036-T-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000388.4(CASR):c.-154T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000156 in 639,682 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
Exomes 𝑓: 0.0000016 ( 0 hom. )
Consequence
CASR
NM_000388.4 5_prime_UTR
NM_000388.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.11
Publications
0 publications found
Genes affected
CASR (HGNC:1514): (calcium sensing receptor) The protein encoded by this gene is a plasma membrane G protein-coupled receptor that senses small changes in circulating calcium concentration. The encoded protein couples this information to intracellular signaling pathways that modify parathyroid hormone secretion or renal cation handling, and thus this protein plays an essential role in maintaining mineral ion homeostasis. Mutations in this gene are a cause of familial hypocalciuric hypercalcemia, neonatal severe hyperparathyroidism, and autosomal dominant hypocalcemia. [provided by RefSeq, Aug 2017]
CASR Gene-Disease associations (from GenCC):
- autosomal dominant hypocalcemia 1Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Illumina, ClinGen, Labcorp Genetics (formerly Invitae)
- familial hypocalciuric hypercalcemia 1Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Illumina, Orphanet, Genomics England PanelApp
- neonatal severe primary hyperparathyroidismInheritance: AR, AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen, Labcorp Genetics (formerly Invitae)
- autosomal dominant hypocalcemiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- epilepsy, idiopathic generalized, susceptibility to, 8Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
- epilepsyInheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000156 AC: 1AN: 639682Hom.: 0 Cov.: 8 AF XY: 0.00000290 AC XY: 1AN XY: 344578 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
639682
Hom.:
Cov.:
8
AF XY:
AC XY:
1
AN XY:
344578
show subpopulations
African (AFR)
AF:
AC:
1
AN:
17566
American (AMR)
AF:
AC:
0
AN:
40422
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
20114
East Asian (EAS)
AF:
AC:
0
AN:
35098
South Asian (SAS)
AF:
AC:
0
AN:
66718
European-Finnish (FIN)
AF:
AC:
0
AN:
37624
Middle Eastern (MID)
AF:
AC:
0
AN:
2554
European-Non Finnish (NFE)
AF:
AC:
0
AN:
386158
Other (OTH)
AF:
AC:
0
AN:
33428
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.