19-38731149-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_144691.4(CAPN12):c.2032G>A(p.Glu678Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000192 in 1,612,986 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144691.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAPN12 | NM_144691.4 | c.2032G>A | p.Glu678Lys | missense_variant | Exon 19 of 21 | ENST00000328867.9 | NP_653292.2 | |
ACTN4 | NM_004924.6 | c.*1717C>T | 3_prime_UTR_variant | Exon 21 of 21 | ENST00000252699.7 | NP_004915.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAPN12 | ENST00000328867.9 | c.2032G>A | p.Glu678Lys | missense_variant | Exon 19 of 21 | 1 | NM_144691.4 | ENSP00000331636.3 | ||
ACTN4 | ENST00000252699.7 | c.*1717C>T | 3_prime_UTR_variant | Exon 21 of 21 | 1 | NM_004924.6 | ENSP00000252699.2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000361 AC: 9AN: 248978Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135222
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1460832Hom.: 0 Cov.: 34 AF XY: 0.0000248 AC XY: 18AN XY: 726690
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152154Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2032G>A (p.E678K) alteration is located in exon 19 (coding exon 19) of the CAPN12 gene. This alteration results from a G to A substitution at nucleotide position 2032, causing the glutamic acid (E) at amino acid position 678 to be replaced by a lysine (K). 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