rs1131611
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002653.5(PITX1):c.418C>A(p.Arg140=) variant causes a synonymous change. The variant allele was found at a frequency of 0.127 in 1,597,336 control chromosomes in the GnomAD database, including 17,408 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.20 ( 4603 hom., cov: 34)
Exomes 𝑓: 0.12 ( 12805 hom. )
Consequence
PITX1
NM_002653.5 synonymous
NM_002653.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 6.58
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 5-135029306-G-T is Benign according to our data. Variant chr5-135029306-G-T is described in ClinVar as [Benign]. Clinvar id is 285760.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-135029306-G-T is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PITX1 | NM_002653.5 | c.418C>A | p.Arg140= | synonymous_variant | 3/3 | ENST00000265340.12 | |
PITX1 | XM_047417318.1 | c.520C>A | p.Arg174= | synonymous_variant | 4/4 | ||
PITX1 | XM_047417319.1 | c.73C>A | p.Arg25= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PITX1 | ENST00000265340.12 | c.418C>A | p.Arg140= | synonymous_variant | 3/3 | 1 | NM_002653.5 | P1 | |
PITX1 | ENST00000506438.5 | c.418C>A | p.Arg140= | synonymous_variant | 4/4 | 1 | P1 | ||
PITX1 | ENST00000503586.1 | n.540C>A | non_coding_transcript_exon_variant | 3/3 | 3 | ||||
PITX1 | ENST00000504936.1 | n.751C>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.199 AC: 30230AN: 152092Hom.: 4568 Cov.: 34
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GnomAD3 exomes AF: 0.123 AC: 28929AN: 235206Hom.: 2911 AF XY: 0.113 AC XY: 14357AN XY: 127284
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GnomAD4 exome AF: 0.119 AC: 172354AN: 1445126Hom.: 12805 Cov.: 35 AF XY: 0.116 AC XY: 83050AN XY: 716832
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GnomAD4 genome ? AF: 0.199 AC: 30338AN: 152210Hom.: 4603 Cov.: 34 AF XY: 0.192 AC XY: 14301AN XY: 74444
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 08, 2016 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 16, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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