chr17-72121467-A-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_000346.4(SOX9):c.76A>G(p.Met26Val) variant causes a missense change. The variant allele was found at a frequency of 0.000274 in 1,612,664 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M26K) has been classified as Uncertain significance.
Frequency
Consequence
NM_000346.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOX9 | NM_000346.4 | c.76A>G | p.Met26Val | missense_variant | 1/3 | ENST00000245479.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOX9 | ENST00000245479.3 | c.76A>G | p.Met26Val | missense_variant | 1/3 | 1 | NM_000346.4 | P1 | |
SOX9-AS1 | ENST00000414600.1 | n.96+20218T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 151986Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000551 AC: 135AN: 244822Hom.: 5 AF XY: 0.000695 AC XY: 93AN XY: 133760
GnomAD4 exome AF: 0.000293 AC: 428AN: 1460560Hom.: 16 Cov.: 31 AF XY: 0.000416 AC XY: 302AN XY: 726616
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152104Hom.: 0 Cov.: 31 AF XY: 0.0000941 AC XY: 7AN XY: 74368
ClinVar
Submissions by phenotype
SOX9-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 11, 2019 | 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). - |
Camptomelic dysplasia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2022 | SOX9: BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at