3-20175019-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001199251.3(SGO1):āc.512T>Cā(p.Val171Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00153 in 1,585,702 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001199251.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SGO1 | NM_001199251.3 | c.512T>C | p.Val171Ala | missense_variant | 6/8 | ENST00000412997.6 | |
SGO1-AS1 | NR_132785.1 | n.324+201A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGO1 | ENST00000412997.6 | c.512T>C | p.Val171Ala | missense_variant | 6/8 | 1 | NM_001199251.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00795 AC: 1209AN: 152164Hom.: 14 Cov.: 32
GnomAD3 exomes AF: 0.00208 AC: 487AN: 234556Hom.: 6 AF XY: 0.00151 AC XY: 192AN XY: 126858
GnomAD4 exome AF: 0.000838 AC: 1201AN: 1433420Hom.: 17 Cov.: 31 AF XY: 0.000734 AC XY: 521AN XY: 710198
GnomAD4 genome AF: 0.00804 AC: 1224AN: 152282Hom.: 15 Cov.: 32 AF XY: 0.00831 AC XY: 619AN XY: 74466
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at