15-80402580-A-T

Variant names:

• chr15-80402580-A-T
• rs2278702
• ENST00000794218.1:n.1148T>A

Variant summary

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

The ENST00000794218.1(ARNT2-DT):​n.1148T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,054 control chromosomes in the GnomAD database, including 4,617 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 0.22 (4617 hom., cov: 32)
• Consequence: ARNT2-DT ENST00000794218.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 14 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARNT2-DT	NR_184067.1	n.572+922T>A		intron_variant	Intron 2 of 4
ARNT2-DT	NR_184068.1	n.290+922T>A		intron_variant	Intron 2 of 4
ARNT2-DT	NR_184069.1	n.572+922T>A		intron_variant	Intron 2 of 5
ARNT2-DT	NR_184070.1	n.290+922T>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARNT2-DT	ENST00000794218.1	n.1148T>A		non_coding_transcript_exon_variant	Exon 2 of 2
ARNT2-DT	ENST00000794220.1	n.1362T>A		non_coding_transcript_exon_variant	Exon 2 of 2
ARNT2-DT	ENST00000559008.2	n.74+922T>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33873 AN: 151936 Hom.: 4608 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0821

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.223 AC: 33906 AN: 152054 Hom.: 4617 Cov.: 32 AF XY: 0.220 AC XY: 16329 AN XY: 74344

African (AFR) AF: 0.383 AC: 15890 AN: 41446

American (AMR) AF: 0.181 AC: 2763 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 521 AN: 3468

East Asian (EAS) AF: 0.170 AC: 877 AN: 5168

South Asian (SAS) AF: 0.0817 AC: 394 AN: 4820

European-Finnish (FIN) AF: 0.196 AC: 2072 AN: 10592

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.160 AC: 10895 AN: 67974

Other (OTH) AF: 0.201 AC: 424 AN: 2114

Alfa AF: 0.201 Hom.: 471

Bravo AF: 0.226

Asia WGS AF: 0.139 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.76
DANN	Benign	0.89
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2278702; hg19: chr15-80694922;