chr3-52525069-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001134231.2(NT5DC2):c.1241C>T(p.Ala414Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000398 in 1,590,486 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A414T) has been classified 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NT5DC2 | NM_001134231.2 | c.1241C>T | p.Ala414Val | missense_variant | 12/14 | ENST00000422318.7 | |
NT5DC2 | NM_022908.3 | c.1130C>T | p.Ala377Val | missense_variant | 12/14 | ||
NT5DC2 | XM_006713303.4 | c.1241C>T | p.Ala414Val | missense_variant | 12/14 | ||
NT5DC2 | XM_047448760.1 | c.1130C>T | p.Ala377Val | missense_variant | 12/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NT5DC2 | ENST00000422318.7 | c.1241C>T | p.Ala414Val | missense_variant | 12/14 | 5 | NM_001134231.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000290 AC: 44AN: 151736Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000213 AC: 43AN: 202010Hom.: 0 AF XY: 0.000207 AC XY: 23AN XY: 110996
GnomAD4 exome AF: 0.000409 AC: 589AN: 1438750Hom.: 0 Cov.: 57 AF XY: 0.000402 AC XY: 287AN XY: 713996
GnomAD4 genome AF: 0.000290 AC: 44AN: 151736Hom.: 0 Cov.: 32 AF XY: 0.000283 AC XY: 21AN XY: 74090
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.1241C>T (p.A414V) alteration is located in exon 12 (coding exon 12) of the NT5DC2 gene. This alteration results from a C to T substitution at nucleotide position 1241, causing the alanine (A) at amino acid position 414 to be replaced by a valine (V). 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