rs2073416
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_005069.6(SIM2):c.1179G>T(p.Ser393=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,449,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_005069.6 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIM2 | NM_005069.6 | c.1179G>T | p.Ser393= | synonymous_variant | 10/11 | ENST00000290399.11 | |
SIM2 | NM_009586.5 | c.1179G>T | p.Ser393= | synonymous_variant | 10/10 | ||
SIM2 | XM_011529694.2 | c.876G>T | p.Ser292= | synonymous_variant | 9/10 | ||
SIM2 | XM_047440952.1 | c.876G>T | p.Ser292= | synonymous_variant | 9/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIM2 | ENST00000290399.11 | c.1179G>T | p.Ser393= | synonymous_variant | 10/11 | 1 | NM_005069.6 | P1 | |
SIM2 | ENST00000431229.1 | c.993G>T | p.Ser331= | synonymous_variant | 9/10 | 1 | |||
SIM2 | ENST00000481185.1 | n.1792G>T | non_coding_transcript_exon_variant | 10/10 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.90e-7 AC: 1AN: 1449902Hom.: 0 Cov.: 34 AF XY: 0.00000139 AC XY: 1AN XY: 720018
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at