1-150842935-G-A

Variant names:

• chr1-150842935-G-A
• rs3768013
• NM_001668.4:c.228-467C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001668.4(ARNT):​c.228-467C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,788 control chromosomes in the GnomAD database, including 13,831 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 0.42 (13831 hom., cov: 31)
• Consequence: ARNT NM_001668.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 24 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001668.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARNT	NM_001668.4	MANE Select	c.228-467C>T		intron	N/A	NP_001659.1	P27540-1
	ARNT	NM_001350225.2		c.225-467C>T		intron	N/A	NP_001337154.1
	ARNT	NM_001286036.2		c.228-467C>T		intron	N/A	NP_001272965.1	P27540-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARNT	ENST00000358595.10	TSL:1 MANE Select	c.228-467C>T		intron	N/A	ENSP00000351407.5	P27540-1
	ARNT	ENST00000354396.6	TSL:1	c.228-467C>T		intron	N/A	ENSP00000346372.2	P27540-4
	ARNT	ENST00000515192.5	TSL:1	c.201-467C>T		intron	N/A	ENSP00000423851.1	P27540-3

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63756 AN: 151670 Hom.: 13818 Cov.: 31

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.419

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.420 AC: 63797 AN: 151788 Hom.: 13831 Cov.: 31 AF XY: 0.423 AC XY: 31410 AN XY: 74188

African (AFR) AF: 0.501 AC: 20724 AN: 41374

American (AMR) AF: 0.444 AC: 6773 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1672 AN: 3468

East Asian (EAS) AF: 0.390 AC: 2008 AN: 5150

South Asian (SAS) AF: 0.543 AC: 2615 AN: 4820

European-Finnish (FIN) AF: 0.344 AC: 3625 AN: 10526

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25124 AN: 67890

Other (OTH) AF: 0.422 AC: 887 AN: 2102

Alfa AF: 0.381 Hom.: 13820

Bravo AF: 0.425

Asia WGS AF: 0.428 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.21
PhyloP100		-0.030
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3768013; hg19: chr1-150815411;