6-21594616-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003107.3(SOX4):āc.82C>Gā(p.Leu28Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00879 in 1,608,160 control chromosomes in the GnomAD database, including 101 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_003107.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00838 AC: 1276AN: 152212Hom.: 14 Cov.: 32
GnomAD3 exomes AF: 0.00795 AC: 1848AN: 232390Hom.: 16 AF XY: 0.00823 AC XY: 1052AN XY: 127816
GnomAD4 exome AF: 0.00884 AC: 12863AN: 1455830Hom.: 87 Cov.: 32 AF XY: 0.00899 AC XY: 6509AN XY: 723968
GnomAD4 genome AF: 0.00838 AC: 1277AN: 152330Hom.: 14 Cov.: 32 AF XY: 0.00850 AC XY: 633AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:2
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SOX4: PP3, BS1, BS2 -
SOX4-related disorder Benign:1
This variant is classified as 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