rs114727970
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_001368809.2(AMPD2):c.1242C>T(p.Tyr414=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00501 in 1,613,894 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.0030 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0052 ( 23 hom. )
Consequence
AMPD2
NM_001368809.2 synonymous
NM_001368809.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.00
Genes affected
AMPD2 (HGNC:469): (adenosine monophosphate deaminase 2) The protein encoded by this gene is important in purine metabolism by converting AMP to IMP. The encoded protein, which acts as a homotetramer, is one of three AMP deaminases found in mammals. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
Variant 1-109628244-C-T is Benign according to our data. Variant chr1-109628244-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 210136.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=2, Likely_benign=1}.
BP7
?
Synonymous conserved (PhyloP=-2 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00303 (462/152320) while in subpopulation NFE AF= 0.00553 (376/68046). AF 95% confidence interval is 0.00506. There are 0 homozygotes in gnomad4. There are 194 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome4 at 23 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMPD2 | NM_001368809.2 | c.1242C>T | p.Tyr414= | synonymous_variant | 11/19 | ENST00000528667.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMPD2 | ENST00000528667.7 | c.1242C>T | p.Tyr414= | synonymous_variant | 11/19 | 1 | NM_001368809.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00304 AC: 462AN: 152202Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00294 AC: 738AN: 251110Hom.: 1 AF XY: 0.00296 AC XY: 402AN XY: 135704
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GnomAD4 exome AF: 0.00522 AC: 7629AN: 1461574Hom.: 23 Cov.: 34 AF XY: 0.00497 AC XY: 3617AN XY: 727062
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GnomAD4 genome ? AF: 0.00303 AC: 462AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.00261 AC XY: 194AN XY: 74464
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:3
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | AMPD2: BP4, BP7 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 16, 2020 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 28, 2015 | - - |
Hereditary spastic paraplegia 63;C4014354:Pontocerebellar hypoplasia type 9 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at