ENST00000559008.2:n.137+899A>G

Variant names:

• chr15-80397045-T-C
• rs17223788
• ENST00000559008.2:n.137+899A>G

Variant summary

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

The ENST00000559008.2(ARNT2-DT):​n.137+899A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,994 control chromosomes in the GnomAD database, including 9,066 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 0.33 (9066 hom., cov: 31)
• Consequence: ARNT2-DT ENST00000559008.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70
• Publications: 5 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARNT2-DT	NR_184067.1	n.635+899A>G		intron_variant	Intron 3 of 4
ARNT2-DT	NR_184068.1	n.353+899A>G		intron_variant	Intron 3 of 4
ARNT2-DT	NR_184069.1	n.635+899A>G		intron_variant	Intron 3 of 5
ARNT2-DT	NR_184070.1	n.353+899A>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARNT2-DT	ENST00000559008.2	n.137+899A>G		intron_variant	Intron 2 of 2	3
ARNT2-DT	ENST00000559267.1	n.64+899A>G		intron_variant	Intron 1 of 2	2
ARNT2-DT	ENST00000653750.2	n.611+899A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49586 AN: 151876 Hom.: 9069 Cov.: 31

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.326 AC: 49584 AN: 151994 Hom.: 9066 Cov.: 31 AF XY: 0.330 AC XY: 24509 AN XY: 74292

African (AFR) AF: 0.182 AC: 7544 AN: 41468

American (AMR) AF: 0.304 AC: 4639 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1029 AN: 3466

East Asian (EAS) AF: 0.650 AC: 3345 AN: 5150

South Asian (SAS) AF: 0.463 AC: 2228 AN: 4812

European-Finnish (FIN) AF: 0.409 AC: 4323 AN: 10562

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25227 AN: 67944

Other (OTH) AF: 0.329 AC: 695 AN: 2112

Alfa AF: 0.340 Hom.: 4505

Bravo AF: 0.311

Asia WGS AF: 0.483 AC: 1678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.071
DANN	Benign	0.38
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs17223788; hg19: chr15-80689387;