rs4678175
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP2BP4_StrongBP6BS1
The ENST00000498619.4(CASR):c.1612C>T(p.Leu538Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,614,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000498619.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CASR | NM_000388.4 | c.1609-27C>T | intron_variant | ENST00000639785.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASR | ENST00000498619.4 | c.1612C>T | p.Leu538Phe | missense_variant | 6/7 | 1 | |||
CASR | ENST00000639785.2 | c.1609-27C>T | intron_variant | 1 | NM_000388.4 | P1 | |||
CASR | ENST00000490131.7 | c.1378-27C>T | intron_variant | 5 | |||||
CASR | ENST00000638421.1 | c.1609-27C>T | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251476Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135912
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461846Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727224
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74372
ClinVar
Submissions by phenotype
Chorea;C0036572:Seizure;C0221356:Brachycephaly;C0557874:Global developmental delay;C1858120:Generalized hypotonia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Personalized Medicine, Children's Hospital Los Angeles | - | - - |
Autosomal dominant hypocalcemia 1;C1809471:Familial hypocalciuric hypercalcemia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at