6-85450183-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002526.4(NT5E):āc.44C>Gā(p.Ala15Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000286 in 1,606,684 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002526.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NT5E | NM_002526.4 | c.44C>G | p.Ala15Gly | missense_variant | 1/9 | ENST00000257770.8 | NP_002517.1 | |
NT5E | NM_001204813.2 | c.44C>G | p.Ala15Gly | missense_variant | 1/8 | NP_001191742.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NT5E | ENST00000257770.8 | c.44C>G | p.Ala15Gly | missense_variant | 1/9 | 1 | NM_002526.4 | ENSP00000257770.3 | ||
NT5E | ENST00000369646.7 | c.44C>G | p.Ala15Gly | missense_variant | 1/3 | 1 | ENSP00000358660.3 | |||
NT5E | ENST00000369651.7 | c.44C>G | p.Ala15Gly | missense_variant | 1/8 | 2 | ENSP00000358665.3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000224 AC: 5AN: 223364Hom.: 0 AF XY: 0.0000243 AC XY: 3AN XY: 123682
GnomAD4 exome AF: 0.0000282 AC: 41AN: 1454498Hom.: 0 Cov.: 32 AF XY: 0.0000332 AC XY: 24AN XY: 723114
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74356
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 21, 2024 | The c.44C>G (p.A15G) alteration is located in exon 1 (coding exon 1) of the NT5E gene. This alteration results from a C to G substitution at nucleotide position 44, causing the alanine (A) at amino acid position 15 to be replaced by a glycine (G). 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