Variant rs3768017 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001668.4(ARNT):c.1168-19T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0875 in 1,569,310 control chromosomes in the GnomAD database, including 6,932 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 0.074 ( 587 hom., cov: 31)

Exomes 𝑓: 0.089 ( 6345 hom. )

Consequence

ARNT
NM_001668.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.830

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARNT	NM_001668.4 linkuse as main transcript	c.1168-19T>G		intron_variant		ENST00000358595.10	NP_001659.1	P27540-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARNT	ENST00000358595.10 linkuse as main transcript	c.1168-19T>G		intron_variant		1	NM_001668.4	ENSP00000351407.5		P27540-1
ARNT	ENST00000471844.6 linkuse as main transcript	n.1168-19T>G		intron_variant		2		ENSP00000425899.1		A6NGV6

Frequencies

GnomAD3 genomes

AF:

0.0740

AC:

11249

AN:

151938

Hom.:

584

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0141

Gnomad AMI

AF:

0.128

Gnomad AMR

AF:

0.0668

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.183

Gnomad SAS

AF:

0.103

Gnomad FIN

AF:

0.0959

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.0939

Gnomad OTH

AF:

0.0746

GnomAD3 exomes

AF:

0.0965

AC:

23341

AN:

241758

Hom.:

1435

AF XY:

0.0996

AC XY:

13087

AN XY:

131402

show subpopulations

Gnomad AFR exome

AF:

0.0122

Gnomad AMR exome

AF:

0.0546

Gnomad ASJ exome

AF:

0.156

Gnomad EAS exome

AF:

0.209

Gnomad SAS exome

AF:

0.108

Gnomad FIN exome

AF:

0.0923

Gnomad NFE exome

AF:

0.0948

Gnomad OTH exome

AF:

0.102

GnomAD4 exome

AF:

0.0890

AC:

126074

AN:

1417252

Hom.:

6345

Cov.:

AF XY:

0.0909

AC XY:

64231

AN XY:

706768

show subpopulations

Gnomad4 AFR exome

AF:

0.0117

Gnomad4 AMR exome

AF:

0.0562

Gnomad4 ASJ exome

AF:

0.151

Gnomad4 EAS exome

AF:

0.183

Gnomad4 SAS exome

AF:

0.106

Gnomad4 FIN exome

AF:

0.0954

Gnomad4 NFE exome

AF:

0.0858

Gnomad4 OTH exome

AF:

0.0892

GnomAD4 genome

AF:

0.0741

AC:

11261

AN:

152058

Hom.:

587

Cov.:

AF XY:

0.0745

AC XY:

5536

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.0140

Gnomad4 AMR

AF:

0.0671

Gnomad4 ASJ

AF:

0.145

Gnomad4 EAS

AF:

0.184

Gnomad4 SAS

AF:

0.103

Gnomad4 FIN

AF:

0.0959

Gnomad4 NFE

AF:

0.0939

Gnomad4 OTH

AF:

0.0762

Alfa

AF:

0.0928

Hom.:

177

Bravo

AF:

0.0718

Asia WGS

AF:

0.139

AC:

484

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

8.7

DANN

Benign

0.54

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