rs9658625
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003578.4(SOAT2):āc.41A>Gā(p.Glu14Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0744 in 1,545,708 control chromosomes in the GnomAD database, including 4,893 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003578.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOAT2 | NM_003578.4 | c.41A>G | p.Glu14Gly | missense_variant | 1/15 | ENST00000301466.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOAT2 | ENST00000301466.8 | c.41A>G | p.Glu14Gly | missense_variant | 1/15 | 1 | NM_003578.4 | P1 | |
SOAT2 | ENST00000551896.5 | c.41A>G | p.Glu14Gly | missense_variant | 1/5 | 2 | |||
SOAT2 | ENST00000542365.1 | c.41A>G | p.Glu14Gly | missense_variant, NMD_transcript_variant | 1/14 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0765 AC: 11632AN: 152038Hom.: 519 Cov.: 32
GnomAD3 exomes AF: 0.0935 AC: 13238AN: 141642Hom.: 712 AF XY: 0.0950 AC XY: 7191AN XY: 75656
GnomAD4 exome AF: 0.0741 AC: 103294AN: 1393552Hom.: 4374 Cov.: 32 AF XY: 0.0756 AC XY: 51995AN XY: 687584
GnomAD4 genome ? AF: 0.0765 AC: 11639AN: 152156Hom.: 519 Cov.: 32 AF XY: 0.0798 AC XY: 5937AN XY: 74390
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at