rs41280332
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001368809.2(AMPD2):c.1407+3A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00391 in 1,612,168 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001368809.2 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AMPD2 | NM_001368809.2 | c.1407+3A>G | splice_region_variant, intron_variant | Intron 12 of 18 | ENST00000528667.7 | NP_001355738.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AMPD2 | ENST00000528667.7 | c.1407+3A>G | splice_region_variant, intron_variant | Intron 12 of 18 | 1 | NM_001368809.2 | ENSP00000436541.2 |
Frequencies
GnomAD3 genomes AF: 0.00296 AC: 450AN: 152030Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00267 AC: 666AN: 249168Hom.: 0 AF XY: 0.00271 AC XY: 366AN XY: 134960
GnomAD4 exome AF: 0.00401 AC: 5853AN: 1460020Hom.: 9 Cov.: 36 AF XY: 0.00388 AC XY: 2819AN XY: 726404
GnomAD4 genome AF: 0.00296 AC: 451AN: 152148Hom.: 2 Cov.: 32 AF XY: 0.00261 AC XY: 194AN XY: 74404
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2024 | AMPD2: BP4, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 30, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 15, 2017 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 28, 2017 | - - |
Hereditary spastic paraplegia 63;C4014354:Pontocerebellar hypoplasia type 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 15, 2025 | - - |
AMPD2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 16, 2020 | 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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at