rs2278702

Positions:

• chr15-80402580-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_184068.1(ARNT2-DT):​n.290+922T>A variant causes a intron, non coding transcript 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 NR_184068.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ARNT2-DT	NR_184068.1	n.290+922T>A		intron_variant, non_coding_transcript_variant
ARNT2-DT	NR_184067.1	n.572+922T>A		intron_variant, non_coding_transcript_variant
ARNT2-DT	NR_184069.1	n.572+922T>A		intron_variant, non_coding_transcript_variant
ARNT2-DT	NR_184070.1	n.290+922T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARNT2-DT	ENST00000656160.1	n.590+922T>A		intron_variant, non_coding_transcript_variant
ARNT2-DT	ENST00000559008.2	n.74+922T>A		intron_variant, non_coding_transcript_variant		3
ARNT2-DT	ENST00000653750.1	n.302+79T>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.0817

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.201

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2278702; hg19: chr15-80694922;