rs6047590
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001257096.2(PAX1):c.1283-1485T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,136 control chromosomes in the GnomAD database, including 5,116 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 0.17 ( 5116 hom., cov: 33)
Consequence
PAX1
NM_001257096.2 intron
NM_001257096.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.14
Genes affected
PAX1 (HGNC:8615): (paired box 1) This gene is a member of the paired box (PAX) family of transcription factors. Members of the PAX family typically contain a paired box domain and a paired-type homeodomain. These genes play critical roles during fetal development. This gene plays a role in pattern formation during embryogenesis and may be essential for development of the vertebral column. This gene is silenced by methylation in ovarian and cervical cancers and may be a tumor suppressor gene. Mutations in this gene are also associated with vertebral malformations. [provided by RefSeq, Mar 2012]
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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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAX1 | NM_001257096.2 | c.1283-1485T>A | intron_variant | ENST00000613128.5 | NP_001244025.1 | |||
PAX1 | NM_006192.5 | c.1283-1495T>A | intron_variant | NP_006183.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAX1 | ENST00000613128.5 | c.1283-1485T>A | intron_variant | 1 | NM_001257096.2 | ENSP00000481334.1 | ||||
PAX1 | ENST00000398485.6 | c.1283-1495T>A | intron_variant | 5 | ENSP00000381499.2 | |||||
PAX1 | ENST00000444366.2 | c.1211-1485T>A | intron_variant | 2 | ENSP00000410355.2 |
Frequencies
GnomAD3 genomes AF: 0.167 AC: 25457AN: 152018Hom.: 5081 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.168 AC: 25537AN: 152136Hom.: 5116 Cov.: 33 AF XY: 0.165 AC XY: 12297AN XY: 74386
GnomAD4 genome
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546
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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