chr10-103449409-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015916.5(CALHM2):c.533G>A(p.Arg178His) variant causes a missense change. The variant allele was found at a frequency of 0.0000508 in 1,612,862 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. R178C) has been classified as Uncertain significance.
Frequency
Consequence
NM_015916.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CALHM2 | NM_015916.5 | c.533G>A | p.Arg178His | missense_variant | 3/4 | ENST00000260743.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CALHM2 | ENST00000260743.10 | c.533G>A | p.Arg178His | missense_variant | 3/4 | 1 | NM_015916.5 | P1 | |
CALHM2 | ENST00000369788.7 | c.533G>A | p.Arg178His | missense_variant | 3/4 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000644 AC: 16AN: 248258Hom.: 0 AF XY: 0.0000741 AC XY: 10AN XY: 134908
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1460554Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 726608
GnomAD4 genome AF: 0.000112 AC: 17AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2022 | The c.533G>A (p.R178H) alteration is located in exon 3 (coding exon 1) of the CALHM2 gene. This alteration results from a G to A substitution at nucleotide position 533, causing the arginine (R) at amino acid position 178 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