1-230691414-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_007357.3(COG2):c.1965C>T(p.Asn655Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,748 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_007357.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COG2 | NM_007357.3 | c.1965C>T | p.Asn655Asn | synonymous_variant | 17/18 | ENST00000366669.9 | NP_031383.1 | |
COG2 | NM_001145036.2 | c.1962C>T | p.Asn654Asn | synonymous_variant | 17/18 | NP_001138508.1 | ||
COG2 | XM_047449445.1 | c.1626C>T | p.Asn542Asn | synonymous_variant | 15/16 | XP_047305401.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461748Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727186
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Congenital disorder of glycosylation, type IIq Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 27, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.