rs1042815
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002145.4(HOXB2):c.*142C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 510,568 control chromosomes in the GnomAD database, including 91,279 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 0.52 ( 22840 hom., cov: 31)
Exomes 𝑓: 0.61 ( 68439 hom. )
Consequence
HOXB2
NM_002145.4 3_prime_UTR
NM_002145.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.15
Genes affected
HOXB2 (HGNC:5113): (homeobox B2) 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 pancreatic cancer. [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=-0.81).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOXB2 | NM_002145.4 | c.*142C>T | 3_prime_UTR_variant | 2/2 | ENST00000330070.6 | ||
HOXB2 | XM_005257275.5 | c.*142C>T | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOXB2 | ENST00000330070.6 | c.*142C>T | 3_prime_UTR_variant | 2/2 | 1 | NM_002145.4 | P1 | ||
HOXB2 | ENST00000504772.3 | n.192+29C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.524 AC: 79604AN: 151868Hom.: 22819 Cov.: 31
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GnomAD4 exome AF: 0.611 AC: 218996AN: 358580Hom.: 68439 Cov.: 5 AF XY: 0.614 AC XY: 112312AN XY: 183052
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GnomAD4 genome ? AF: 0.524 AC: 79651AN: 151988Hom.: 22840 Cov.: 31 AF XY: 0.529 AC XY: 39312AN XY: 74288
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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