rs2270916
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000388.4(CASR):c.1732+16T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 1,613,346 control chromosomes in the GnomAD database, including 17,374 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000388.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CASR | ENST00000639785.2 | c.1732+16T>C | intron_variant | Intron 6 of 6 | 1 | NM_000388.4 | ENSP00000491584.2 | |||
CASR | ENST00000498619.4 | c.1762+16T>C | intron_variant | Intron 6 of 6 | 1 | ENSP00000420194.1 | ||||
CASR | ENST00000638421.1 | c.1732+16T>C | intron_variant | Intron 6 of 6 | 5 | ENSP00000492190.1 | ||||
CASR | ENST00000490131.7 | c.1501+16T>C | intron_variant | Intron 4 of 4 | 5 | ENSP00000418685.2 |
Frequencies
GnomAD3 genomes AF: 0.116 AC: 17650AN: 152104Hom.: 1362 Cov.: 32
GnomAD3 exomes AF: 0.130 AC: 32638AN: 251462Hom.: 3085 AF XY: 0.126 AC XY: 17157AN XY: 135904
GnomAD4 exome AF: 0.137 AC: 200715AN: 1461126Hom.: 16015 Cov.: 32 AF XY: 0.134 AC XY: 97454AN XY: 726880
GnomAD4 genome AF: 0.116 AC: 17642AN: 152220Hom.: 1359 Cov.: 32 AF XY: 0.117 AC XY: 8712AN XY: 74416
ClinVar
Submissions by phenotype
not specified Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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not provided Benign:2
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Autosomal dominant hypocalcemia 1;C1809471:Familial hypocalciuric hypercalcemia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at