2-230169166-A-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_080424.4(SP110):c.2100T>C(p.Gly700Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000514 in 1,613,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_080424.4 synonymous
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: 0.0000263 AC: 4AN: 152020Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000131 AC: 33AN: 251426Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135878
GnomAD4 exome AF: 0.0000540 AC: 79AN: 1461782Hom.: 0 Cov.: 30 AF XY: 0.0000770 AC XY: 56AN XY: 727210
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152020Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74258
ClinVar
Submissions by phenotype
SP110-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Hepatic veno-occlusive disease-immunodeficiency syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at