chr11-10456392-G-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001025389.2(AMPD3):c.-6+944G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000674 in 1,613,844 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0030 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00044 ( 2 hom. )
Consequence
AMPD3
NM_001025389.2 intron
NM_001025389.2 intron
Scores
2
12
Clinical Significance
Conservation
PhyloP100: -1.06
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 Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0044176877).
BP6
?
Variant 11-10456392-G-T is Benign according to our data. Variant chr11-10456392-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 3035621.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAdExome at 2 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMPD3 | NM_001025389.2 | c.-6+944G>T | intron_variant | ENST00000396553.7 | |||
AMPD3 | NM_001025390.2 | c.6G>T | p.Glu2Asp | missense_variant | 1/15 | ||
AMPD3 | NM_000480.3 | c.23-5123G>T | intron_variant | ||||
AMPD3 | NM_001172431.2 | c.-277-5123G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMPD3 | ENST00000396553.7 | c.-6+944G>T | intron_variant | 1 | NM_001025389.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00290 AC: 442AN: 152256Hom.: 1 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000800 AC: 199AN: 248686Hom.: 2 AF XY: 0.000697 AC XY: 94AN XY: 134938
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GnomAD4 exome AF: 0.000435 AC: 636AN: 1461470Hom.: 2 Cov.: 30 AF XY: 0.000377 AC XY: 274AN XY: 727022
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GnomAD4 genome ? AF: 0.00296 AC: 451AN: 152374Hom.: 1 Cov.: 32 AF XY: 0.00278 AC XY: 207AN XY: 74510
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
AMPD3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 04, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Vest4
MutPred
Loss of glycosylation at P3 (P = 0.1056);
MVP
ClinPred
T
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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