5-135033743-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_ModerateBS2
The NM_002653.5(PITX1):c.139G>T(p.Ala47Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000346 in 1,443,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002653.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PITX1 | NM_002653.5 | c.139G>T | p.Ala47Ser | missense_variant | Exon 1 of 3 | ENST00000265340.12 | NP_002644.4 | |
PITX1 | XM_047417318.1 | c.241G>T | p.Ala81Ser | missense_variant | Exon 2 of 4 | XP_047273274.1 | ||
PITX1-AS1 | NR_161235.1 | n.267+203C>A | intron_variant | Intron 1 of 5 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000461 AC: 1AN: 217076Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 121488
GnomAD4 exome AF: 0.00000346 AC: 5AN: 1443678Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1AN XY: 718566
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not provided Uncertain:1
Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis supports that this variant does not alter splicing; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at