NM_002653.5:c.*57_*62dupGCGCGG
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002653.5(PITX1):c.*57_*62dupGCGCGG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000073 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000063 ( 0 hom. )
Consequence
PITX1
NM_002653.5 3_prime_UTR
NM_002653.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.756
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 -4 ACMG points.
BS2
High AC in GnomAd4 at 11 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PITX1 | NM_002653.5 | c.*57_*62dupGCGCGG | 3_prime_UTR_variant | Exon 3 of 3 | ENST00000265340.12 | NP_002644.4 | ||
PITX1 | XM_047417318.1 | c.*57_*62dupGCGCGG | 3_prime_UTR_variant | Exon 4 of 4 | XP_047273274.1 | |||
PITX1 | XM_047417319.1 | c.*57_*62dupGCGCGG | 3_prime_UTR_variant | Exon 3 of 3 | XP_047273275.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000735 AC: 11AN: 149724Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0000628 AC: 69AN: 1098046Hom.: 0 Cov.: 0 AF XY: 0.0000605 AC XY: 32AN XY: 528894
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GnomAD4 genome AF: 0.0000734 AC: 11AN: 149826Hom.: 0 Cov.: 0 AF XY: 0.0000821 AC XY: 6AN XY: 73126
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at