chr10-103089674-A-ATTC
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3
The NM_001351169.2(NT5C2):c.1681_1683dupGAA(p.Glu561dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000066 in 151,556 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001351169.2 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NT5C2 | NM_001351169.2 | c.1681_1683dupGAA | p.Glu561dup | conservative_inframe_insertion | Exon 19 of 19 | ENST00000404739.8 | NP_001338098.1 | |
CNNM2 | NM_017649.5 | c.*12498_*12500dupTTC | 3_prime_UTR_variant | Exon 8 of 8 | ENST00000369878.9 | NP_060119.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NT5C2 | ENST00000404739.8 | c.1681_1683dupGAA | p.Glu561dup | conservative_inframe_insertion | Exon 19 of 19 | 1 | NM_001351169.2 | ENSP00000383960.3 | ||
CNNM2 | ENST00000369878.9 | c.*12498_*12500dupTTC | 3_prime_UTR_variant | Exon 8 of 8 | 1 | NM_017649.5 | ENSP00000358894.3 |
Frequencies
GnomAD3 genomes AF: 0.00000660 AC: 1AN: 151556Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome AF: 0.00000660 AC: 1AN: 151556Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 73956
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 45 Uncertain:1
Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. This variant has not been reported in the literature in individuals affected with NT5C2-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.01%). This sequence change disrupts the translational stop signal of the NT5C2 mRNA. It is expected to extend the length of the NT5C2 protein by 1 additional amino acid residues. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at