2-44942121-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_005413.4(SIX3):c.17C>T(p.Pro6Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000689 in 1,595,788 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005413.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152010Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000426 AC: 1AN: 234568Hom.: 0 AF XY: 0.00000779 AC XY: 1AN XY: 128432
GnomAD4 exome AF: 0.00000693 AC: 10AN: 1443662Hom.: 0 Cov.: 32 AF XY: 0.00000835 AC XY: 6AN XY: 718704
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74368
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.17C>T (p.P6L) alteration is located in exon 1 (coding exon 1) of the SIX3 gene. This alteration results from a C to T substitution at nucleotide position 17, causing the proline (P) at amino acid position 6 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