chr7-33014823-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BS1_Supporting
The NM_001002010.5(NT5C3A):c.903G>C(p.Glu301Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000238 in 1,611,264 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001002010.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000112 AC: 28AN: 249852Hom.: 0 AF XY: 0.0000961 AC XY: 13AN XY: 135236
GnomAD4 exome AF: 0.000245 AC: 358AN: 1459128Hom.: 0 Cov.: 31 AF XY: 0.000248 AC XY: 180AN XY: 725996
GnomAD4 genome AF: 0.000171 AC: 26AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.801G>C (p.E267D) alteration is located in exon 10 (coding exon 9) of the NT5C3A gene. This alteration results from a G to C substitution at nucleotide position 801, causing the glutamic acid (E) at amino acid position 267 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency Uncertain:1
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not provided Uncertain:1
This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 267 of the NT5C3A protein (p.Glu267Asp). This variant is present in population databases (rs138845909, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with NT5C3A-related conditions. ClinVar contains an entry for this variant (Variation ID: 2070549). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt NT5C3A protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at