Variant chr15-80347222-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.214

Variant links:

Genes affected

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

ARNT2-DT links:

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ACMG classification

Classification made for transcript

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	Effect
ARNT2-DT	NR_184068.1 linkuse as main transcript	n.439+477A>G	intron_variant, non_coding_transcript_variant
ARNT2-DT	NR_184067.1 linkuse as main transcript	n.721+477A>G	intron_variant, non_coding_transcript_variant
ARNT2-DT	NR_184069.1 linkuse as main transcript	n.860+477A>G	intron_variant, non_coding_transcript_variant
ARNT2-DT	NR_184070.1 linkuse as main transcript	n.575+477A>G	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ARNT2-DT	ENST00000656160.1 linkuse as main transcript	n.739+477A>G	intron_variant, non_coding_transcript_variant
ARNT2-DT	ENST00000559267.1 linkuse as main transcript	n.161+466A>G	intron_variant, non_coding_transcript_variant	2
ARNT2-DT	ENST00000653750.1 linkuse as main transcript	n.451+477A>G	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.464

AC:

70501

AN:

151786

Hom.:

16722

Cov.:

show subpopulations

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.:

AF XY:

0.467

AC XY:

34700

AN XY:

74246

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over