rs150001655
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_018714.3(COG1):āc.529A>Gā(p.Ile177Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000983 in 1,613,850 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_018714.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COG1 | NM_018714.3 | c.529A>G | p.Ile177Val | missense_variant | 2/14 | ENST00000299886.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COG1 | ENST00000299886.9 | c.529A>G | p.Ile177Val | missense_variant | 2/14 | 1 | NM_018714.3 | P1 | |
COG1 | ENST00000438720.7 | c.529A>G | p.Ile177Val | missense_variant | 2/13 | 1 | |||
COG1 | ENST00000582587.2 | c.*153A>G | 3_prime_UTR_variant, NMD_transcript_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00499 AC: 759AN: 152046Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00137 AC: 343AN: 250278Hom.: 4 AF XY: 0.000953 AC XY: 129AN XY: 135422
GnomAD4 exome AF: 0.000564 AC: 824AN: 1461686Hom.: 6 Cov.: 63 AF XY: 0.000483 AC XY: 351AN XY: 727172
GnomAD4 genome ? AF: 0.00501 AC: 762AN: 152164Hom.: 6 Cov.: 33 AF XY: 0.00448 AC XY: 333AN XY: 74384
ClinVar
Submissions by phenotype
COG1 congenital disorder of glycosylation Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 07, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Sep 02, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at