rs140850664
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_005169.4(PHOX2A):c.-19G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.000035 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00064 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PHOX2A
NM_005169.4 5_prime_UTR
NM_005169.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.62
Genes affected
PHOX2A (HGNC:691): (paired like homeobox 2A) The protein encoded by this gene contains a paired-like homeodomain most similar to that of the Drosophila aristaless gene product. The encoded protein plays a central role in development of the autonomic nervous system. It regulates the expression of tyrosine hydroxylase and dopamine beta-hydroxylase, two catecholaminergic biosynthetic enzymes essential for the differentiation and maintenance of the noradrenergic neurotransmitter phenotype. The encoded protein has also been shown to regulate transcription of the alpha3 nicotinic acetylcholine receptor gene. Mutations in this gene have been associated with autosomal recessive congenital fibrosis of the extraocular muscles. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHOX2A | NM_005169.4 | c.-19G>C | 5_prime_UTR_variant | 1/3 | ENST00000298231.5 | ||
PHOX2A | XM_047426947.1 | c.-19G>C | 5_prime_UTR_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHOX2A | ENST00000298231.5 | c.-19G>C | 5_prime_UTR_variant | 1/3 | 1 | NM_005169.4 | P1 | ||
PHOX2A | ENST00000544057.1 | n.85+1557G>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 4AN: 112762Hom.: 0 Cov.: 30 FAILED QC
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GnomAD4 exome AF: 0.000643 AC: 171AN: 265900Hom.: 0 Cov.: 6 AF XY: 0.000668 AC XY: 85AN XY: 127282
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000355 AC: 4AN: 112762Hom.: 0 Cov.: 30 AF XY: 0.0000180 AC XY: 1AN XY: 55604
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ClinVar
Not reported inComputational scores
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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