chr3-122284684-C-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.Pro910=) 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 (★★). Synonymous variant affecting the same amino acid position (i.e. P910P) has been classified 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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CASR | NM_000388.4 | c.2730C>A | p.Pro910= | synonymous_variant | 7/7 | ENST00000639785.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASR | ENST00000639785.2 | c.2730C>A | p.Pro910= | synonymous_variant | 7/7 | 1 | NM_000388.4 | P1 | |
CASR | ENST00000498619.4 | c.2760C>A | p.Pro920= | synonymous_variant | 7/7 | 1 | |||
CASR | ENST00000638421.1 | c.2730C>A | p.Pro910= | synonymous_variant | 7/7 | 5 | P1 | ||
CASR | ENST00000490131.7 | c.2499C>A | p.Pro833= | synonymous_variant | 5/5 | 5 |
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 specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Aug 15, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 29, 2014 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 30, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 30, 2018 | 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. - |
Nephrolithiasis/nephrocalcinosis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 26, 2019 | 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
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Benign, criteria provided, single submitter | curation | Sema4, Sema4 | Sep 01, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at