15-42652576-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_020759.3(STARD9):c.686C>T(p.Thr229Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000475 in 1,537,468 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T229K) has been classified as Uncertain significance.
Frequency
Consequence
NM_020759.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STARD9 | ENST00000290607.12 | c.686C>T | p.Thr229Met | missense_variant | Exon 9 of 33 | 5 | NM_020759.3 | ENSP00000290607.7 | ||
STARD9 | ENST00000564158.5 | n.743C>T | non_coding_transcript_exon_variant | Exon 9 of 14 | 1 | |||||
STARD9 | ENST00000568493.1 | n.757C>T | non_coding_transcript_exon_variant | Exon 7 of 11 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000210 AC: 3AN: 143196Hom.: 0 AF XY: 0.0000131 AC XY: 1AN XY: 76376
GnomAD4 exome AF: 0.0000469 AC: 65AN: 1385164Hom.: 0 Cov.: 30 AF XY: 0.0000541 AC XY: 37AN XY: 683490
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152304Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.686C>T (p.T229M) alteration is located in exon 9 (coding exon 9) of the STARD9 gene. This alteration results from a C to T substitution at nucleotide position 686, causing the threonine (T) at amino acid position 229 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at