chr2-96827754-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_017623.5(CNNM3):c.1543C>T(p.Arg515Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,613,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017623.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251066Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135720
GnomAD4 exome AF: 0.0000410 AC: 60AN: 1461736Hom.: 0 Cov.: 31 AF XY: 0.0000399 AC XY: 29AN XY: 727168
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1543C>T (p.R515C) alteration is located in exon 4 (coding exon 4) of the CNNM3 gene. This alteration results from a C to T substitution at nucleotide position 1543, causing the arginine (R) at amino acid position 515 to be replaced by a cysteine (C). 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