NM_031431.4:c.5C>T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PM2BP4_Strong
The NM_031431.4(COG3):c.5C>T(p.Ala2Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000169 in 1,571,412 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 Uncertain significance (★).
Frequency
Consequence
NM_031431.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COG3 | NM_031431.4 | c.5C>T | p.Ala2Val | missense_variant | Exon 1 of 23 | ENST00000349995.10 | NP_113619.3 | |
COG3 | XM_047430702.1 | c.5C>T | p.Ala2Val | missense_variant | Exon 1 of 19 | XP_047286658.1 | ||
COG3 | XR_007063702.1 | n.103C>T | non_coding_transcript_exon_variant | Exon 1 of 14 | ||||
COG3 | XR_429222.5 | n.103C>T | non_coding_transcript_exon_variant | Exon 1 of 24 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000156 AC: 28AN: 179562Hom.: 0 AF XY: 0.000143 AC XY: 14AN XY: 97964
GnomAD4 exome AF: 0.000178 AC: 252AN: 1419166Hom.: 0 Cov.: 30 AF XY: 0.000175 AC XY: 123AN XY: 702416
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.5C>T (p.A2V) alteration is located in exon 1 (coding exon 1) of the COG3 gene. This alteration results from a C to T substitution at nucleotide position 5, causing the alanine (A) at amino acid position 2 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at