rs3809782
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001384749.1(HOXB3):c.-424-6551C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 151,688 control chromosomes in the GnomAD database, including 29,802 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 0.62 ( 29793 hom., cov: 29)
Exomes 𝑓: 0.77 ( 9 hom. )
Consequence
HOXB3
NM_001384749.1 intron
NM_001384749.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.01
Genes affected
HOXB3 (HGNC:5114): (homeobox B3) This gene is a member of the Antp homeobox family and encodes a nuclear protein with a homeobox DNA-binding domain. It is included in a cluster of homeobox B genes located on chromosome 17. The encoded protein functions as a sequence-specific transcription factor that is involved in development. Increased expression of this gene is associated with a distinct biologic subset of acute myeloid leukemia (AML). [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=-0.53).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOXB3 | NM_001384749.1 | c.-424-6551C>T | intron_variant | ENST00000498678.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOXB3 | ENST00000498678.6 | c.-424-6551C>T | intron_variant | 2 | NM_001384749.1 | P1 | |||
ENST00000548801.1 | n.1695C>T | non_coding_transcript_exon_variant | 1/1 | ||||||
HOXB-AS3 | ENST00000465846.6 | n.78-19882G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.625 AC: 94661AN: 151544Hom.: 29778 Cov.: 29
GnomAD3 genomes
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GnomAD4 exome AF: 0.769 AC: 20AN: 26Hom.: 9 Cov.: 0 AF XY: 0.667 AC XY: 12AN XY: 18
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GnomAD4 genome ? AF: 0.624 AC: 94712AN: 151662Hom.: 29793 Cov.: 29 AF XY: 0.623 AC XY: 46180AN XY: 74114
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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