17-72121407-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_000346.4(SOX9):c.16C>T(p.Pro6Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,612,586 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P6P) has been classified as Likely benign.
Frequency
Consequence
NM_000346.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOX9 | NM_000346.4 | c.16C>T | p.Pro6Ser | missense_variant | 1/3 | ENST00000245479.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOX9 | ENST00000245479.3 | c.16C>T | p.Pro6Ser | missense_variant | 1/3 | 1 | NM_000346.4 | P1 | |
SOX9-AS1 | ENST00000414600.1 | n.96+20278G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152166Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000204 AC: 5AN: 244860Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134058
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1460420Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 726532
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152166Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 9AN XY: 74322
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 07, 2022 | The c.16C>T (p.P6S) alteration is located in exon 1 (coding exon 1) of the SOX9 gene. This alteration results from a C to T substitution at nucleotide position 16, causing the proline (P) at amino acid position 6 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Camptomelic dysplasia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at