1-109621124-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001308170.1(AMPD2):āc.17C>Gā(p.Ala6Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000321 in 1,599,162 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_001308170.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AMPD2 | NM_001368809.2 | c.-52C>G | 5_prime_UTR_variant | Exon 2 of 19 | ENST00000528667.7 | NP_001355738.1 | ||
AMPD2 | NM_001308170.1 | c.17C>G | p.Ala6Gly | missense_variant | Exon 1 of 17 | NP_001295099.1 | ||
AMPD2 | NM_139156.4 | c.10+846C>G | intron_variant | Intron 1 of 17 | NP_631895.1 | |||
AMPD2 | NM_004037.9 | c.-52C>G | upstream_gene_variant | NP_004028.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AMPD2 | ENST00000528667 | c.-52C>G | 5_prime_UTR_variant | Exon 2 of 19 | 1 | NM_001368809.2 | ENSP00000436541.2 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000737 AC: 161AN: 218376Hom.: 1 AF XY: 0.000975 AC XY: 117AN XY: 119970
GnomAD4 exome AF: 0.000338 AC: 489AN: 1446932Hom.: 8 Cov.: 34 AF XY: 0.000497 AC XY: 357AN XY: 718928
GnomAD4 genome AF: 0.000164 AC: 25AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74430
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 63;C4014354:Pontocerebellar hypoplasia type 9 Benign:1
- -
not provided Benign:1
AMPD2: BP4, BP7 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at