chr19-38731181-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_144691.4(CAPN12):c.2000G>A(p.Arg667His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000391 in 1,612,888 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R667C) has been classified as Benign.
Frequency
Consequence
NM_144691.4 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 |
---|---|---|---|---|---|---|---|---|
CAPN12 | NM_144691.4 | c.2000G>A | p.Arg667His | missense_variant | Exon 19 of 21 | ENST00000328867.9 | NP_653292.2 | |
ACTN4 | NM_004924.6 | c.*1749C>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.2000G>A | p.Arg667His | missense_variant | Exon 19 of 21 | 1 | NM_144691.4 | ENSP00000331636.3 | ||
ACTN4 | ENST00000252699.7 | c.*1749C>T | 3_prime_UTR_variant | Exon 21 of 21 | 1 | NM_004924.6 | ENSP00000252699.2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000643 AC: 16AN: 248970Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135304
GnomAD4 exome AF: 0.0000390 AC: 57AN: 1460698Hom.: 0 Cov.: 34 AF XY: 0.0000468 AC XY: 34AN XY: 726636
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2000G>A (p.R667H) 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 2000, causing the arginine (R) at amino acid position 667 to be replaced by a histidine (H). 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