7-33014505-T-TAAGA
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001002010.5(NT5C3A):c.*224_*225insTCTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.75 ( 39596 hom., cov: 0)
Exomes 𝑓: 0.66 ( 77715 hom. )
Failed GnomAD Quality Control
Consequence
NT5C3A
NM_001002010.5 3_prime_UTR
NM_001002010.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.699
Genes affected
NT5C3A (HGNC:17820): (5'-nucleotidase, cytosolic IIIA) This gene encodes a member of the 5'-nucleotidase family of enzymes that catalyze the dephosphorylation of nucleoside 5'-monophosphates. The encoded protein is the type 1 isozyme of pyrimidine 5' nucleotidase and catalyzes the dephosphorylation of pyrimidine 5' monophosphates. Mutations in this gene are a cause of hemolytic anemia due to uridine 5-prime monophosphate hydrolase deficiency. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and pseudogenes of this gene are located on the long arm of chromosomes 3 and 4. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 7-33014505-T-TAAGA is Benign according to our data. Variant chr7-33014505-T-TAAGA is described in ClinVar as [Benign]. Clinvar id is 1289594.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NT5C3A | NM_001002010.5 | c.*224_*225insTCTT | 3_prime_UTR_variant | 9/9 | ENST00000610140.7 | NP_001002010.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NT5C3A | ENST00000610140.7 | c.*224_*225insTCTT | 3_prime_UTR_variant | 9/9 | 1 | NM_001002010.5 | ENSP00000476480.2 |
Frequencies
GnomAD3 genomes AF: 0.754 AC: 108944AN: 144406Hom.: 39553 Cov.: 0
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GnomAD3 exomes AF: 0.612 AC: 51064AN: 83480Hom.: 14778 AF XY: 0.602 AC XY: 26980AN XY: 44784
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.665 AC: 263928AN: 396958Hom.: 77715 Cov.: 6 AF XY: 0.662 AC XY: 142678AN XY: 215398
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GnomAD4 genome AF: 0.755 AC: 109043AN: 144518Hom.: 39596 Cov.: 0 AF XY: 0.756 AC XY: 53338AN XY: 70546
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at