Variant rs3215133 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001668.4(ARNT):c.1032+107del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0953 in 1,210,486 control chromosomes in the GnomAD database, including 6,760 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.081 ( 750 hom., cov: 31)

Exomes 𝑓: 0.097 ( 6010 hom. )

Consequence

ARNT
NM_001668.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.23

Variant links:

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]

ARNT links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARNT	NM_001668.4 linkuse as main transcript	c.1032+107del		intron_variant		ENST00000358595.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARNT	ENST00000358595.10 linkuse as main transcript	c.1032+107del		intron_variant		1	NM_001668.4	P3	P27540-1

Frequencies

GnomAD3 genomes

AF:

0.0812

AC:

12359

AN:

152162

Hom.:

747

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0202

Gnomad AMI

AF:

0.0758

Gnomad AMR

AF:

0.148

Gnomad ASJ

AF:

0.0383

Gnomad EAS

AF:

0.00423

Gnomad SAS

AF:

0.0294

Gnomad FIN

AF:

0.167

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.103

Gnomad OTH

AF:

0.0662

GnomAD4 exome

AF:

0.0974

AC:

103032

AN:

1058206

Hom.:

6010

AF XY:

0.0946

AC XY:

50470

AN XY:

533544

show subpopulations

Gnomad4 AFR exome

AF:

0.0169

Gnomad4 AMR exome

AF:

0.183

Gnomad4 ASJ exome

AF:

0.0375

Gnomad4 EAS exome

AF:

0.00910

Gnomad4 SAS exome

AF:

0.0337

Gnomad4 FIN exome

AF:

0.166

Gnomad4 NFE exome

AF:

0.105

Gnomad4 OTH exome

AF:

0.0840

GnomAD4 genome

AF:

0.0812

AC:

12363

AN:

152280

Hom.:

750

Cov.:

AF XY:

0.0852

AC XY:

6343

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.0202

Gnomad4 AMR

AF:

0.148

Gnomad4 ASJ

AF:

0.0383

Gnomad4 EAS

AF:

0.00424

Gnomad4 SAS

AF:

0.0286

Gnomad4 FIN

AF:

0.167

Gnomad4 NFE

AF:

0.103

Gnomad4 OTH

AF:

0.0655

Alfa

AF:

0.0384

Hom.:

Bravo

AF:

0.0781

Asia WGS

AF:

0.0180

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over