chr15-80470185-TC-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_014862.4(ARNT2):c.195-28del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.79 ( 47425 hom., cov: 0)
Exomes 𝑓: 0.77 ( 426178 hom. )
Consequence
ARNT2
NM_014862.4 intron
NM_014862.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.00400
Genes affected
ARNT2 (HGNC:16876): (aryl hydrocarbon receptor nuclear translocator 2) This gene encodes a member of the basic-helix-loop-helix-Per-Arnt-Sim (bHLH-PAS) superfamily of transcription factors. The encoded protein acts as a partner for several sensor proteins of the bHLH-PAS family, forming heterodimers with the sensor proteins that bind regulatory DNA sequences in genes responsive to developmental and environmental stimuli. Under hypoxic conditions, the encoded protein complexes with hypoxia-inducible factor 1alpha in the nucleus and this complex binds to hypoxia-responsive elements in enhancers and promoters of oxygen-responsive genes. A highly similar protein in mouse forms functional complexes with both aryl hydrocarbon receptors and Single-minded proteins, suggesting additional roles for the encoded protein in the metabolism of xenobiotic compounds and the regulation of neurogenesis, respectively. [provided by RefSeq, Dec 2013]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 15-80470185-TC-T is Benign according to our data. Variant chr15-80470185-TC-T is described in ClinVar as [Benign]. Clinvar id is 1192449.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARNT2 | NM_014862.4 | c.195-28del | intron_variant | ENST00000303329.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARNT2 | ENST00000303329.9 | c.195-28del | intron_variant | 1 | NM_014862.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.788 AC: 119741AN: 151926Hom.: 47384 Cov.: 0
GnomAD3 genomes
?
AF:
AC:
119741
AN:
151926
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.778 AC: 180696AN: 232372Hom.: 70708 AF XY: 0.774 AC XY: 96722AN XY: 125010
GnomAD3 exomes
AF:
AC:
180696
AN:
232372
Hom.:
AF XY:
AC XY:
96722
AN XY:
125010
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.769 AC: 1103885AN: 1434822Hom.: 426178 Cov.: 0 AF XY: 0.768 AC XY: 547793AN XY: 713242
GnomAD4 exome
AF:
AC:
1103885
AN:
1434822
Hom.:
Cov.:
0
AF XY:
AC XY:
547793
AN XY:
713242
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.788 AC: 119834AN: 152044Hom.: 47425 Cov.: 0 AF XY: 0.789 AC XY: 58659AN XY: 74304
GnomAD4 genome
?
AF:
AC:
119834
AN:
152044
Hom.:
Cov.:
0
AF XY:
AC XY:
58659
AN XY:
74304
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Webb-Dattani syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at