rs78018362
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP7
The NM_005413.4(SIX3):c.90G>A(p.Ala30=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000626 in 1,596,704 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. Synonymous variant affecting the same amino acid position (i.e. A30A) has been classified as Benign.
Frequency
Consequence
NM_005413.4 synonymous
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 |
---|---|---|---|---|---|---|---|
SIX3 | NM_005413.4 | c.90G>A | p.Ala30= | synonymous_variant | 1/2 | ENST00000260653.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIX3 | ENST00000260653.5 | c.90G>A | p.Ala30= | synonymous_variant | 1/2 | 1 | NM_005413.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000661 AC: 1AN: 151384Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000128 AC: 3AN: 234134Hom.: 0 AF XY: 0.00000780 AC XY: 1AN XY: 128228
GnomAD4 exome AF: 0.00000623 AC: 9AN: 1445320Hom.: 0 Cov.: 32 AF XY: 0.00000278 AC XY: 2AN XY: 719436
GnomAD4 genome ? AF: 0.00000661 AC: 1AN: 151384Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73870
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at