1-109621090-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001368809.2(AMPD2):c.-86G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000746 in 1,608,600 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001368809.2 5_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AMPD2 | NM_001368809.2 | c.-86G>A | 5_prime_UTR_variant | Exon 2 of 19 | ENST00000528667.7 | NP_001355738.1 | ||
AMPD2 | NM_001308170.1 | c.-18G>A | 5_prime_UTR_variant | Exon 1 of 17 | NP_001295099.1 | |||
AMPD2 | NM_139156.4 | c.10+812G>A | intron_variant | Intron 1 of 17 | NP_631895.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AMPD2 | ENST00000528667 | c.-86G>A | 5_prime_UTR_variant | Exon 2 of 19 | 1 | NM_001368809.2 | ENSP00000436541.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152250Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000846 AC: 2AN: 236340Hom.: 0 AF XY: 0.00000771 AC XY: 1AN XY: 129690
GnomAD4 exome AF: 0.00000755 AC: 11AN: 1456350Hom.: 0 Cov.: 35 AF XY: 0.00000690 AC XY: 5AN XY: 724188
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74372
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.77G>A (p.G26E) alteration is located in exon 1 (coding exon 1) of the AMPD2 gene. This alteration results from a G to A substitution at nucleotide position 77, causing the glycine (G) at amino acid position 26 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at