rs370941478
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_005413.4(SIX3):c.831G>A(p.Pro277=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000405 in 1,578,362 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P277P) has been classified as Likely benign.
Frequency
Consequence
NM_005413.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIX3 | NM_005413.4 | c.831G>A | p.Pro277= | synonymous_variant | 2/2 | ENST00000260653.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIX3 | ENST00000260653.5 | c.831G>A | p.Pro277= | synonymous_variant | 2/2 | 1 | NM_005413.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000212 AC: 41AN: 193448Hom.: 0 AF XY: 0.000176 AC XY: 19AN XY: 107866
GnomAD4 exome AF: 0.000427 AC: 609AN: 1426144Hom.: 0 Cov.: 31 AF XY: 0.000421 AC XY: 298AN XY: 708180
GnomAD4 genome AF: 0.000204 AC: 31AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74370
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Holoprosencephaly 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 06, 2022 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | SIX3: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at