chr3-58505281-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003500.4(ACOX2):c.1989C>T(p.Asn663=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,638 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 Likely benign (★).
Frequency
Consequence
NM_003500.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACOX2 | NM_003500.4 | c.1989C>T | p.Asn663= | synonymous_variant | 15/15 | ENST00000302819.10 | |
ACOX2 | XM_047449042.1 | c.2187C>T | p.Asn729= | synonymous_variant | 15/15 | ||
ACOX2 | XM_005265505.2 | c.1989C>T | p.Asn663= | synonymous_variant | 15/15 | ||
ACOX2 | XM_006713340.4 | c.1695C>T | p.Asn565= | synonymous_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACOX2 | ENST00000302819.10 | c.1989C>T | p.Asn663= | synonymous_variant | 15/15 | 1 | NM_003500.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459638Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 725996
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 02, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.