1-230759544-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_006615.3(CAPN9):c.316C>T(p.Leu106Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000617 in 1,459,546 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006615.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAPN9 | ENST00000271971.7 | c.316C>T | p.Leu106Phe | missense_variant | Exon 3 of 20 | 1 | NM_006615.3 | ENSP00000271971.2 | ||
CAPN9 | ENST00000354537.1 | c.316C>T | p.Leu106Phe | missense_variant | Exon 3 of 19 | 1 | ENSP00000346538.1 | |||
CAPN9 | ENST00000366666.6 | c.214-3109C>T | intron_variant | Intron 1 of 17 | 1 | ENSP00000355626.2 | ||||
ENSG00000244137 | ENST00000412344.1 | n.380+35569G>A | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000617 AC: 9AN: 1459546Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 725976
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.316C>T (p.L106F) alteration is located in exon 3 (coding exon 3) of the CAPN9 gene. This alteration results from a C to T substitution at nucleotide position 316, causing the leucine (L) at amino acid position 106 to be replaced by a phenylalanine (F). 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