20-36794109-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_080627.4(SOGA1):c.3973G>A(p.Gly1325Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000122 in 1,551,318 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SOGA1 | NM_080627.4 | c.3973G>A | p.Gly1325Arg | missense_variant | 14/15 | ENST00000237536.9 | NP_542194.2 | |
SOGA1 | NM_199181.3 | c.2993+266G>A | intron_variant | NP_954650.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SOGA1 | ENST00000237536.9 | c.3973G>A | p.Gly1325Arg | missense_variant | 14/15 | 5 | NM_080627.4 | ENSP00000237536 | P2 | |
SOGA1 | ENST00000279034.10 | c.2993+266G>A | intron_variant | 5 | ENSP00000279034 | A2 | ||||
SOGA1 | ENST00000465671.1 | c.2815G>A | p.Gly939Arg | missense_variant, NMD_transcript_variant | 10/12 | 2 | ENSP00000433939 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000643 AC: 1AN: 155466Hom.: 0 AF XY: 0.0000121 AC XY: 1AN XY: 82552
GnomAD4 exome AF: 0.0000114 AC: 16AN: 1399078Hom.: 0 Cov.: 31 AF XY: 0.0000130 AC XY: 9AN XY: 690040
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 03, 2022 | The c.3973G>A (p.G1325R) alteration is located in exon 14 (coding exon 14) of the SOGA1 gene. This alteration results from a G to A substitution at nucleotide position 3973, causing the glycine (G) at amino acid position 1325 to be replaced by an arginine (R). 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