chr1-223717790-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PM2BP4_Strong
The NM_001748.5(CAPN2):āc.266T>Cā(p.Ile89Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000135 in 1,614,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001748.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAPN2 | NM_001748.5 | c.266T>C | p.Ile89Thr | missense_variant | 2/21 | ENST00000295006.6 | |
CAPN2 | NM_001146068.2 | c.32T>C | p.Ile11Thr | missense_variant | 2/21 | ||
CAPN2 | XM_047431344.1 | c.266T>C | p.Ile89Thr | missense_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAPN2 | ENST00000295006.6 | c.266T>C | p.Ile89Thr | missense_variant | 2/21 | 1 | NM_001748.5 | P1 | |
CAPN2 | ENST00000433674.6 | c.32T>C | p.Ile11Thr | missense_variant | 2/21 | 2 | |||
CAPN2 | ENST00000434648.5 | c.32T>C | p.Ile11Thr | missense_variant | 2/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000215 AC: 54AN: 251368Hom.: 0 AF XY: 0.000213 AC XY: 29AN XY: 135850
GnomAD4 exome AF: 0.000139 AC: 203AN: 1461818Hom.: 0 Cov.: 30 AF XY: 0.000128 AC XY: 93AN XY: 727210
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 12, 2023 | The c.266T>C (p.I89T) alteration is located in exon 2 (coding exon 2) of the CAPN2 gene. This alteration results from a T to C substitution at nucleotide position 266, causing the isoleucine (I) at amino acid position 89 to be replaced by a threonine (T). 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