chr1-24533201-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_013441.4(RCAN3):c.488C>T(p.Ala163Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000106 in 1,605,650 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013441.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RCAN3 | NM_013441.4 | c.488C>T | p.Ala163Val | missense_variant | Exon 4 of 5 | ENST00000374395.9 | NP_038469.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000246 AC: 6AN: 243894Hom.: 0 AF XY: 0.0000303 AC XY: 4AN XY: 132158
GnomAD4 exome AF: 0.00000757 AC: 11AN: 1453462Hom.: 0 Cov.: 32 AF XY: 0.0000111 AC XY: 8AN XY: 722968
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.488C>T (p.A163V) alteration is located in exon 4 (coding exon 3) of the RCAN3 gene. This alteration results from a C to T substitution at nucleotide position 488, causing the alanine (A) at amino acid position 163 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at