chr3-52525048-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001134231.2(NT5DC2):c.1262G>A(p.Arg421His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000015 in 1,599,794 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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.1262G>A | p.Arg421His | missense_variant | 12/14 | ENST00000422318.7 | |
NT5DC2 | NM_022908.3 | c.1151G>A | p.Arg384His | missense_variant | 12/14 | ||
NT5DC2 | XM_006713303.4 | c.1262G>A | p.Arg421His | missense_variant | 12/14 | ||
NT5DC2 | XM_047448760.1 | c.1151G>A | p.Arg384His | missense_variant | 12/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NT5DC2 | ENST00000422318.7 | c.1262G>A | p.Arg421His | missense_variant | 12/14 | 5 | NM_001134231.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152114Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000276 AC: 6AN: 217122Hom.: 0 AF XY: 0.0000336 AC XY: 4AN XY: 118966
GnomAD4 exome AF: 0.0000124 AC: 18AN: 1447680Hom.: 0 Cov.: 57 AF XY: 0.0000125 AC XY: 9AN XY: 719106
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152114Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 14, 2023 | The c.1262G>A (p.R421H) alteration is located in exon 12 (coding exon 12) of the NT5DC2 gene. This alteration results from a G to A substitution at nucleotide position 1262, causing the arginine (R) at amino acid position 421 to be replaced by a histidine (H). 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