3-20174605-T-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001199251.3(SGO1):āc.926A>Gā(p.Tyr309Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000298 in 1,601,064 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001199251.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00150 AC: 228AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000394 AC: 91AN: 230950Hom.: 0 AF XY: 0.000312 AC XY: 39AN XY: 124942
GnomAD4 exome AF: 0.000172 AC: 249AN: 1448724Hom.: 3 Cov.: 31 AF XY: 0.000133 AC XY: 96AN XY: 720040
GnomAD4 genome AF: 0.00150 AC: 228AN: 152340Hom.: 0 Cov.: 32 AF XY: 0.00137 AC XY: 102AN XY: 74502
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: Gupta2013[Computational]) -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at