rs6872664
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002653.5(PITX1):c.170-400G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 229,816 control chromosomes in the GnomAD database, including 5,215 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.20 ( 4603 hom., cov: 33)
Exomes 𝑓: 0.10 ( 612 hom. )
Consequence
PITX1
NM_002653.5 intron
NM_002653.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.443
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PITX1 | NM_002653.5 | c.170-400G>A | intron_variant | ENST00000265340.12 | |||
PITX1 | XM_047417318.1 | c.272-400G>A | intron_variant | ||||
PITX1 | XM_047417319.1 | c.-176-400G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PITX1 | ENST00000265340.12 | c.170-400G>A | intron_variant | 1 | NM_002653.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.199 AC: 30225AN: 152060Hom.: 4568 Cov.: 33
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GnomAD4 exome AF: 0.100 AC: 7775AN: 77638Hom.: 612 Cov.: 0 AF XY: 0.0964 AC XY: 3859AN XY: 40012
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GnomAD4 genome ? AF: 0.199 AC: 30333AN: 152178Hom.: 4603 Cov.: 33 AF XY: 0.192 AC XY: 14295AN XY: 74414
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at