chr6-85485261-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_002526.4(NT5E):c.778G>C(p.Ala260Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NT5E | NM_002526.4 | c.778G>C | p.Ala260Pro | missense_variant | 4/9 | ENST00000257770.8 | |
NT5E | NM_001204813.2 | c.778G>C | p.Ala260Pro | missense_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NT5E | ENST00000257770.8 | c.778G>C | p.Ala260Pro | missense_variant | 4/9 | 1 | NM_002526.4 | P1 | |
NT5E | ENST00000369651.7 | c.778G>C | p.Ala260Pro | missense_variant | 4/8 | 2 | |||
NT5E | ENST00000416334.5 | c.73G>C | p.Ala25Pro | missense_variant | 2/5 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461852Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727230
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 02, 2023 | The c.778G>C (p.A260P) alteration is located in exon 4 (coding exon 4) of the NT5E gene. This alteration results from a G to C substitution at nucleotide position 778, causing the alanine (A) at amino acid position 260 to be replaced by a proline (P). 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
Publications
No publications associated with this variant yet.