1-109621015-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001368809.2(AMPD2):c.-161T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,114 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001368809.2 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AMPD2 | NM_001368809.2 | c.-161T>G | 5_prime_UTR_variant | Exon 2 of 19 | ENST00000528667.7 | NP_001355738.1 | ||
AMPD2 | NM_001308170.1 | c.-93T>G | 5_prime_UTR_variant | Exon 1 of 17 | NP_001295099.1 | |||
AMPD2 | NM_139156.4 | c.10+737T>G | 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.-161T>G | 5_prime_UTR_variant | Exon 2 of 19 | 1 | NM_001368809.2 | ENSP00000436541.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000445 AC: 1AN: 224788Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 122224
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000112 AC: 160AN: 1429446Hom.: 0 Cov.: 34 AF XY: 0.0000932 AC XY: 66AN XY: 708376
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74310
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 63;C4014354:Pontocerebellar hypoplasia type 9 Uncertain:1
This sequence change affects the initiator methionine of the AMPD2 mRNA. The next in-frame methionine is located at codon 55. This variant is present in population databases (rs769851350, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with AMPD2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1484677). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at