2-277003-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000272065.10(ACP1):āc.317A>Gā(p.Gln106Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 1,598,632 control chromosomes in the GnomAD database, including 89,383 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
ENST00000272065.10 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ACP1 | NM_004300.4 | c.317A>G | p.Gln106Arg | missense_variant | 5/6 | ENST00000272065.10 | NP_004291.1 | |
ACP1 | NM_007099.4 | c.317A>G | p.Gln106Arg | missense_variant | 5/6 | NP_009030.1 | ||
ACP1 | NR_024080.2 | n.364A>G | non_coding_transcript_exon_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACP1 | ENST00000272065.10 | c.317A>G | p.Gln106Arg | missense_variant | 5/6 | 1 | NM_004300.4 | ENSP00000272065 | P3 |
Frequencies
GnomAD3 genomes AF: 0.295 AC: 44899AN: 152026Hom.: 6950 Cov.: 33
GnomAD3 exomes AF: 0.310 AC: 76287AN: 245720Hom.: 12201 AF XY: 0.314 AC XY: 41674AN XY: 132876
GnomAD4 exome AF: 0.333 AC: 482181AN: 1446486Hom.: 82440 Cov.: 30 AF XY: 0.333 AC XY: 239998AN XY: 719940
GnomAD4 genome AF: 0.295 AC: 44897AN: 152146Hom.: 6943 Cov.: 33 AF XY: 0.296 AC XY: 22035AN XY: 74366
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
ACID PHOSPHATASE 1, SOLUBLE, A/B POLYMORPHISM OF Benign:1
Benign, no assertion criteria provided | literature only | OMIM | Aug 12, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at