chr3-52528638-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001134231.2(NT5DC2):āc.547A>Gā(p.Arg183Gly) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001134231.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NT5DC2 | NM_001134231.2 | c.547A>G | p.Arg183Gly | missense_variant, splice_region_variant | 4/14 | ENST00000422318.7 | |
NT5DC2 | NM_022908.3 | c.436A>G | p.Arg146Gly | missense_variant, splice_region_variant | 4/14 | ||
NT5DC2 | XM_006713303.4 | c.547A>G | p.Arg183Gly | missense_variant, splice_region_variant | 4/14 | ||
NT5DC2 | XM_047448760.1 | c.436A>G | p.Arg146Gly | missense_variant, splice_region_variant | 4/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NT5DC2 | ENST00000422318.7 | c.547A>G | p.Arg183Gly | missense_variant, splice_region_variant | 4/14 | 5 | NM_001134231.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152022Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1428476Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 707592
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152022Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74258
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 17, 2022 | The c.547A>G (p.R183G) alteration is located in exon 4 (coding exon 4) of the NT5DC2 gene. This alteration results from a A to G substitution at nucleotide position 547, causing the arginine (R) at amino acid position 183 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