chrX-154830732-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001162936.4(SMIM9):c.125C>T(p.Ser42Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000764 in 1,165,563 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 30 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001162936.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMIM9 | NM_001162936.4 | c.125C>T | p.Ser42Leu | missense_variant | 3/5 | ENST00000369529.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMIM9 | ENST00000369529.2 | c.125C>T | p.Ser42Leu | missense_variant | 3/5 | 5 | NM_001162936.4 | P1 | |
SMIM9 | ENST00000478043.1 | n.434C>T | non_coding_transcript_exon_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000179 AC: 2AN: 111550Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33754
GnomAD3 exomes AF: 0.0000966 AC: 11AN: 113905Hom.: 0 AF XY: 0.0000998 AC XY: 4AN XY: 40091
GnomAD4 exome AF: 0.0000825 AC: 87AN: 1053957Hom.: 0 Cov.: 29 AF XY: 0.0000871 AC XY: 30AN XY: 344453
GnomAD4 genome ? AF: 0.0000179 AC: 2AN: 111606Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33820
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 27, 2022 | The c.125C>T (p.S42L) alteration is located in exon 3 (coding exon 1) of the SMIM9 gene. This alteration results from a C to T substitution at nucleotide position 125, causing the serine (S) at amino acid position 42 to be replaced by a leucine (L). 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