16-67645614-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001013838.3(CARMIL2):c.115G>A(p.Val39Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,506 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001013838.3 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 |
---|---|---|---|---|---|---|---|
CARMIL2 | NM_001013838.3 | c.115G>A | p.Val39Met | missense_variant | 2/38 | ENST00000334583.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CARMIL2 | ENST00000334583.11 | c.115G>A | p.Val39Met | missense_variant | 2/38 | 1 | NM_001013838.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000525 AC: 8AN: 152264Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248288Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134888
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461242Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 726908
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152264Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74388
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Feb 22, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with CARMIL2-related conditions. This variant is present in population databases (rs370315873, gnomAD 0.02%). This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 39 of the CARMIL2 protein (p.Val39Met). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at