chr1-208027330-C-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_025179.4(PLXNA2):c.5598G>C(p.Gly1866Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000713 in 1,612,688 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_025179.4 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: 0.000361 AC: 55AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000113 AC: 28AN: 247904Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 134308
GnomAD4 exome AF: 0.0000411 AC: 60AN: 1460406Hom.: 1 Cov.: 30 AF XY: 0.0000358 AC XY: 26AN XY: 726570
GnomAD4 genome AF: 0.000361 AC: 55AN: 152282Hom.: 0 Cov.: 33 AF XY: 0.000349 AC XY: 26AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:1
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PLXNA2-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at