10-5525410-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005185.4(CALML3):c.325G>A(p.Val109Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000682 in 1,613,910 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005185.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CALML3 | NM_005185.4 | c.325G>A | p.Val109Ile | missense_variant | Exon 1 of 1 | ENST00000315238.3 | NP_005176.1 | |
CALML3-AS1 | NR_120496.1 | n.114+723C>T | intron_variant | Intron 1 of 3 | ||||
CALML3-AS1 | NR_120497.1 | n.114+723C>T | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250574Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135676
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461584Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727130
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.325G>A (p.V109I) alteration is located in exon 1 (coding exon 1) of the CALML3 gene. This alteration results from a G to A substitution at nucleotide position 325, causing the valine (V) at amino acid position 109 to be replaced by an isoleucine (I). 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