NM_005413.4:c.831G>A
Variant summary
Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS1
The NM_005413.4(SIX3):c.831G>A(p.Pro277Pro) 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
Publications
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ACMG classification
Our verdict: Benign. The variant received -15 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SIX3 | ENST00000260653.5 | c.831G>A | p.Pro277Pro | synonymous_variant | Exon 2 of 2 | 1 | NM_005413.4 | ENSP00000260653.3 | ||
SIX3-AS1 | ENST00000760561.1 | n.160C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | ||||||
ENSG00000225156 | ENST00000760330.1 | n.135+10216G>A | intron_variant | Intron 1 of 1 | ||||||
SIX3-AS1 | ENST00000760560.1 | n.388+806C>T | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152218Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.000212 AC: 41AN: 193448 AF XY: 0.000176 show subpopulations
GnomAD4 exome AF: 0.000427 AC: 609AN: 1426144Hom.: 0 Cov.: 31 AF XY: 0.000421 AC XY: 298AN XY: 708180 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000204 AC: 31AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74370 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Benign:1
- -
Holoprosencephaly 2 Benign:1
- -
not provided Benign:1
SIX3: BP4, BP7 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at