5-135033813-TGGCGGC-TGGCGGCGGCGGC
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4BS2
The NM_002653.5(PITX1):c.63_68dupGCCGCC(p.Pro22_Pro23dup) variant causes a disruptive inframe insertion change. The variant allele was found at a frequency of 0.0000187 in 1,553,548 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
PITX1
NM_002653.5 disruptive_inframe_insertion
NM_002653.5 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.71
Genes affected
PITX1 (HGNC:9004): (paired like homeodomain 1) This gene encodes a member of the RIEG/PITX homeobox family, which is in the bicoid class of homeodomain proteins. Members of this family are involved in organ development and left-right asymmetry. This protein acts as a transcriptional regulator involved in basal and hormone-regulated activity of prolactin. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_002653.5.
BS2
High AC in GnomAd4 at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PITX1 | NM_002653.5 | c.63_68dupGCCGCC | p.Pro22_Pro23dup | disruptive_inframe_insertion | Exon 1 of 3 | ENST00000265340.12 | NP_002644.4 | |
PITX1 | XM_047417318.1 | c.165_170dupGCCGCC | p.Pro56_Pro57dup | disruptive_inframe_insertion | Exon 2 of 4 | XP_047273274.1 | ||
PITX1-AS1 | NR_161235.1 | n.267+283_267+288dupGGCGGC | intron_variant | Intron 1 of 5 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000331 AC: 5AN: 151168Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000127 AC: 2AN: 158042Hom.: 0 AF XY: 0.0000112 AC XY: 1AN XY: 89438
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GnomAD4 exome AF: 0.0000171 AC: 24AN: 1402380Hom.: 0 Cov.: 31 AF XY: 0.0000216 AC XY: 15AN XY: 695836
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GnomAD4 genome AF: 0.0000331 AC: 5AN: 151168Hom.: 0 Cov.: 31 AF XY: 0.0000407 AC XY: 3AN XY: 73764
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at