20-36786588-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_080627.4(MTCL2):c.4883G>A(p.Arg1628Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000477 in 1,550,794 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080627.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SOGA1 | ENST00000237536.9 | c.4883G>A | p.Arg1628Gln | missense_variant | Exon 15 of 15 | 5 | NM_080627.4 | ENSP00000237536.4 | ||
SOGA1 | ENST00000279034.10 | c.2993+7787G>A | intron_variant | Intron 14 of 14 | 5 | ENSP00000279034.5 | ||||
SOGA1 | ENST00000465671.1 | n.3722G>A | non_coding_transcript_exon_variant | Exon 11 of 12 | 2 | ENSP00000433939.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151960Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000132 AC: 2AN: 151958Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 80742
GnomAD4 exome AF: 0.0000493 AC: 69AN: 1398834Hom.: 0 Cov.: 33 AF XY: 0.0000391 AC XY: 27AN XY: 689854
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151960Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74214
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4883G>A (p.R1628Q) alteration is located in exon 15 (coding exon 15) of the SOGA1 gene. This alteration results from a G to A substitution at nucleotide position 4883, causing the arginine (R) at amino acid position 1628 to be replaced by a glutamine (Q). 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