rs3848198

Variant names:

• chr15-80347222-T-C
• rs3848198
• ENST00000559267.1:n.161+466A>G

Variant summary

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

The ENST00000559267.1(ARNT2-DT):​n.161+466A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,902 control chromosomes in the GnomAD database, including 16,742 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 0.46 (16742 hom., cov: 32)
• Consequence: ARNT2-DT ENST00000559267.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 1 publications found

Genes affected

ARNT2-DT (HGNC:56077): (ARNT2 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559267.1. 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
	ARNT2-DT	NR_184067.1		n.721+477A>G		intron	N/A
	ARNT2-DT	NR_184068.1		n.439+477A>G		intron	N/A
	ARNT2-DT	NR_184069.1		n.860+477A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARNT2-DT	ENST00000559267.1	TSL:2	n.161+466A>G		intron	N/A
	ARNT2-DT	ENST00000653750.2		n.697+477A>G		intron	N/A
	ARNT2-DT	ENST00000656160.2		n.739+477A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70501 AN: 151786 Hom.: 16722 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.464 AC: 70552 AN: 151902 Hom.: 16742 Cov.: 32 AF XY: 0.467 AC XY: 34700 AN XY: 74246

African (AFR) AF: 0.494 AC: 20471 AN: 41416

American (AMR) AF: 0.560 AC: 8561 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1380 AN: 3468

East Asian (EAS) AF: 0.710 AC: 3666 AN: 5166

South Asian (SAS) AF: 0.524 AC: 2528 AN: 4822

European-Finnish (FIN) AF: 0.401 AC: 4226 AN: 10546

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28211 AN: 67892

Other (OTH) AF: 0.472 AC: 998 AN: 2114

Alfa AF: 0.439 Hom.: 19397

Bravo AF: 0.478

Asia WGS AF: 0.590 AC: 2051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.3
DANN	Benign	0.84
PhyloP100		0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3848198;

hg19: chr15-80639564;