chr11-10455403-AGCCAGC-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_001025389.2(AMPD3):c.-48_-43del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00123 in 985,268 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00060 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0014 ( 2 hom. )
Consequence
AMPD3
NM_001025389.2 5_prime_UTR
NM_001025389.2 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.28
Genes affected
AMPD3 (HGNC:470): (adenosine monophosphate deaminase 3) This gene encodes a member of the AMP deaminase gene family. The encoded protein is a highly regulated enzyme that catalyzes the hydrolytic deamination of adenosine monophosphate to inosine monophosphate, a branch point in the adenylate catabolic pathway. This gene encodes the erythrocyte (E) isoforms, whereas other family members encode isoforms that predominate in muscle (M) and liver (L) cells. Mutations in this gene lead to the clinically asymptomatic, autosomal recessive condition erythrocyte AMP deaminase deficiency. Alternatively spliced transcript variants encoding different isoforms of this gene have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMPD3 | NM_001025389.2 | c.-48_-43del | 5_prime_UTR_variant | 1/15 | ENST00000396553.7 | ||
AMPD3 | NM_000480.3 | c.22+4363_22+4368del | intron_variant | ||||
AMPD3 | NM_001172431.2 | c.-278+4891_-278+4896del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMPD3 | ENST00000396553.7 | c.-48_-43del | 5_prime_UTR_variant | 1/15 | 1 | NM_001025389.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000599 AC: 91AN: 151940Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.00135 AC: 1125AN: 833210Hom.: 2 AF XY: 0.00139 AC XY: 536AN XY: 384800
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GnomAD4 genome ? AF: 0.000598 AC: 91AN: 152058Hom.: 0 Cov.: 31 AF XY: 0.000565 AC XY: 42AN XY: 74352
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Erythrocyte AMP deaminase deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at