chr1-230759604-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006615.3(CAPN9):c.376G>A(p.Gly126Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000392 in 1,607,014 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAPN9 | NM_006615.3 | c.376G>A | p.Gly126Ser | missense_variant | 3/20 | ENST00000271971.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAPN9 | ENST00000271971.7 | c.376G>A | p.Gly126Ser | missense_variant | 3/20 | 1 | NM_006615.3 | P1 | |
CAPN9 | ENST00000354537.1 | c.376G>A | p.Gly126Ser | missense_variant | 3/19 | 1 | |||
CAPN9 | ENST00000366666.6 | c.214-3049G>A | intron_variant | 1 | |||||
ENST00000412344.1 | n.380+35509C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000410 AC: 1AN: 244082Hom.: 0 AF XY: 0.00000758 AC XY: 1AN XY: 131938
GnomAD4 exome AF: 0.0000412 AC: 60AN: 1454832Hom.: 0 Cov.: 30 AF XY: 0.0000304 AC XY: 22AN XY: 723600
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 31, 2023 | The c.376G>A (p.G126S) alteration is located in exon 3 (coding exon 3) of the CAPN9 gene. This alteration results from a G to A substitution at nucleotide position 376, causing the glycine (G) at amino acid position 126 to be replaced by a serine (S). 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