rs10305749
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001668.4(ARNT):c.*6T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000588 in 1,534,374 control chromosomes in the GnomAD database, including 2 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 0.0034 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00028 ( 0 hom. )
Consequence
ARNT
NM_001668.4 3_prime_UTR
NM_001668.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.19
Genes affected
ARNT (HGNC:700): (aryl hydrocarbon receptor nuclear translocator) This gene encodes a protein containing a basic helix-loop-helix domain and two characteristic PAS domains along with a PAC domain. The encoded protein binds to ligand-bound aryl hydrocarbon receptor and aids in the movement of this complex to the nucleus, where it promotes the expression of genes involved in xenobiotic metabolism. This protein is also a co-factor for transcriptional regulation by hypoxia-inducible factor 1. Chromosomal translocation of this locus with the ETV6 (ets variant 6) gene on chromosome 12 have been described in leukemias. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.26).
BS2
?
High AC in GnomAd4 at 513 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARNT | NM_001668.4 | c.*6T>C | 3_prime_UTR_variant | 22/22 | ENST00000358595.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARNT | ENST00000358595.10 | c.*6T>C | 3_prime_UTR_variant | 22/22 | 1 | NM_001668.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00337 AC: 513AN: 152218Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.000822 AC: 172AN: 209140Hom.: 0 AF XY: 0.000605 AC XY: 69AN XY: 113988
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GnomAD4 exome AF: 0.000281 AC: 389AN: 1382038Hom.: 0 Cov.: 29 AF XY: 0.000239 AC XY: 164AN XY: 685774
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GnomAD4 genome ? AF: 0.00337 AC: 513AN: 152336Hom.: 2 Cov.: 32 AF XY: 0.00330 AC XY: 246AN XY: 74494
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at