chr15-80347222-T-C

Position:

• chr15-80347222-T-C

Variant summary

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

The NR_184068.1(ARNT2-DT):​n.439+477A>G 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 0.464 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 NR_184068.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARNT2-DT	NR_184068.1	n.439+477A>G		intron_variant, non_coding_transcript_variant
ARNT2-DT	NR_184067.1	n.721+477A>G		intron_variant, non_coding_transcript_variant
ARNT2-DT	NR_184069.1	n.860+477A>G		intron_variant, non_coding_transcript_variant
ARNT2-DT	NR_184070.1	n.575+477A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARNT2-DT	ENST00000656160.1	n.739+477A>G		intron_variant, non_coding_transcript_variant
ARNT2-DT	ENST00000559267.1	n.161+466A>G		intron_variant, non_coding_transcript_variant		2
ARNT2-DT	ENST00000653750.1	n.451+477A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.472

Alfa AF: 0.436 Hom.: 14741

Bravo AF: 0.478

Asia WGS AF: 0.590 AC: 2051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3848198; hg19: chr15-80639564;