NM_000388.4:c.2730C>A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000388.4(CASR):c.2730C>A(p.Pro910Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000454 in 1,613,544 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000388.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CASR | ENST00000639785.2 | c.2730C>A | p.Pro910Pro | synonymous_variant | Exon 7 of 7 | 1 | NM_000388.4 | ENSP00000491584.2 | ||
CASR | ENST00000498619.4 | c.2760C>A | p.Pro920Pro | synonymous_variant | Exon 7 of 7 | 1 | ENSP00000420194.1 | |||
CASR | ENST00000638421.1 | c.2730C>A | p.Pro910Pro | synonymous_variant | Exon 7 of 7 | 5 | ENSP00000492190.1 | |||
CASR | ENST00000490131.7 | c.2499C>A | p.Pro833Pro | synonymous_variant | Exon 5 of 5 | 5 | ENSP00000418685.2 |
Frequencies
GnomAD3 genomes AF: 0.00208 AC: 316AN: 152224Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000558 AC: 140AN: 250778Hom.: 0 AF XY: 0.000413 AC XY: 56AN XY: 135608
GnomAD4 exome AF: 0.000281 AC: 410AN: 1461202Hom.: 4 Cov.: 70 AF XY: 0.000246 AC XY: 179AN XY: 726790
GnomAD4 genome AF: 0.00211 AC: 322AN: 152342Hom.: 1 Cov.: 33 AF XY: 0.00195 AC XY: 145AN XY: 74508
ClinVar
Submissions by phenotype
not provided Benign:3
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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. -
not specified Benign:2
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Nephrolithiasis/nephrocalcinosis Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Autosomal dominant hypocalcemia 1;C1809471:Familial hypocalciuric hypercalcemia Benign:1
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Hereditary cancer-predisposing syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at