6-85467120-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002526.4(NT5E):c.400G>C(p.Glu134Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,614,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002526.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NT5E | ENST00000257770.8 | c.400G>C | p.Glu134Gln | missense_variant | Exon 2 of 9 | 1 | NM_002526.4 | ENSP00000257770.3 | ||
NT5E | ENST00000369646.7 | c.400G>C | p.Glu134Gln | missense_variant | Exon 2 of 3 | 1 | ENSP00000358660.3 | |||
NT5E | ENST00000369651.7 | c.400G>C | p.Glu134Gln | missense_variant | Exon 2 of 8 | 2 | ENSP00000358665.3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152168Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461872Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727234
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74336
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.400G>C (p.E134Q) alteration is located in exon 2 (coding exon 2) of the NT5E gene. This alteration results from a G to C substitution at nucleotide position 400, causing the glutamic acid (E) at amino acid position 134 to be replaced by a glutamine (Q). 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