6-21594597-C-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_003107.3(SOX4):c.63C>A(p.Asp21Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,609,062 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 (no stars).
Frequency
Consequence
NM_003107.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000604 AC: 92AN: 152212Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000150 AC: 35AN: 234024Hom.: 0 AF XY: 0.000116 AC XY: 15AN XY: 129058
GnomAD4 exome AF: 0.0000632 AC: 92AN: 1456732Hom.: 0 Cov.: 32 AF XY: 0.0000497 AC XY: 36AN XY: 724410
GnomAD4 genome AF: 0.000604 AC: 92AN: 152330Hom.: 1 Cov.: 32 AF XY: 0.000591 AC XY: 44AN XY: 74478
ClinVar
Submissions by phenotype
SOX4-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