1-114684369-C-CA
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP6BS1
The NM_000036.3(AMPD1):c.382-6_382-5insT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0398 in 961,800 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 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_000036.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMPD1 | NM_000036.3 | c.382-6_382-5insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000520113.7 | |||
AMPD1 | NM_001172626.2 | c.370-6_370-5insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMPD1 | ENST00000520113.7 | c.382-6_382-5insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000036.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00114 AC: 153AN: 134380Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0461 AC: 38149AN: 827386Hom.: 0 Cov.: 0 AF XY: 0.0444 AC XY: 18359AN XY: 413154
GnomAD4 genome AF: 0.00113 AC: 152AN: 134414Hom.: 0 Cov.: 32 AF XY: 0.00128 AC XY: 83AN XY: 64854
ClinVar
Submissions by phenotype
Muscle AMP deaminase deficiency Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 12, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at