chr3-52524838-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001134231.2(NT5DC2):c.1391T>A(p.Met464Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,612,466 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001134231.2 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 | UniProt |
---|---|---|---|---|---|---|---|
NT5DC2 | NM_001134231.2 | c.1391T>A | p.Met464Lys | missense_variant | 13/14 | ENST00000422318.7 | |
NT5DC2 | NM_022908.3 | c.1280T>A | p.Met427Lys | missense_variant | 13/14 | ||
NT5DC2 | XM_006713303.4 | c.1391T>A | p.Met464Lys | missense_variant | 13/14 | ||
NT5DC2 | XM_047448760.1 | c.1280T>A | p.Met427Lys | missense_variant | 13/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NT5DC2 | ENST00000422318.7 | c.1391T>A | p.Met464Lys | missense_variant | 13/14 | 5 | NM_001134231.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152032Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 244406Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 132922
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460434Hom.: 0 Cov.: 71 AF XY: 0.00000551 AC XY: 4AN XY: 726496
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152032Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74258
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | The c.1391T>A (p.M464K) alteration is located in exon 13 (coding exon 13) of the NT5DC2 gene. This alteration results from a T to A substitution at nucleotide position 1391, causing the methionine (M) at amino acid position 464 to be replaced by a lysine (K). 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