chrX-154829534-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001162936.4(SMIM9):c.272+1G>A variant causes a splice donor change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000204 in 1,164,650 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 75 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_001162936.4 splice_donor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMIM9 | NM_001162936.4 | c.272+1G>A | splice_donor_variant | ENST00000369529.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMIM9 | ENST00000369529.2 | c.272+1G>A | splice_donor_variant | 5 | NM_001162936.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000152 AC: 17AN: 111566Hom.: 0 Cov.: 23 AF XY: 0.0000889 AC XY: 3AN XY: 33756
GnomAD3 exomes AF: 0.000133 AC: 15AN: 112735Hom.: 0 AF XY: 0.000127 AC XY: 5AN XY: 39297
GnomAD4 exome AF: 0.000210 AC: 221AN: 1053084Hom.: 0 Cov.: 30 AF XY: 0.000209 AC XY: 72AN XY: 343776
GnomAD4 genome ? AF: 0.000152 AC: 17AN: 111566Hom.: 0 Cov.: 23 AF XY: 0.0000889 AC XY: 3AN XY: 33756
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at