Variant rs8034564 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_126453.2(IRAIN):n.3416C>T 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 0.645 in 152,096 control chromosomes in the GnomAD database, including 32,766 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 0.65 ( 32756 hom., cov: 32)

Exomes 𝑓: 0.66 ( 10 hom. )

Consequence

IRAIN
NR_126453.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0230

Variant links:

Genes affected

IRAIN (HGNC:50365): (IGF1R antisense imprinted non-protein coding RNA) This gene expresses a long non-coding RNA in antisense to the insulin-like growth factor type I receptor (IGF1R) gene. This transcript is imprinted and expressed from the paternal allele. It interacts with chromatin and may promote long-range DNA interactions that influence the regulation of gene expression. [provided by RefSeq, Nov 2015]

IRAIN 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=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IRAIN	NR_126453.2 linkuse as main transcript	n.3416C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
IRAIN	ENST00000692203.1 linkuse as main transcript	n.13C>T	non_coding_transcript_exon_variant	1/2
IRAIN	ENST00000687383.1 linkuse as main transcript	n.18C>T	non_coding_transcript_exon_variant	1/1
IRAIN	ENST00000560221.1 linkuse as main transcript		upstream_gene_variant		5

Frequencies

GnomAD3 genomes

AF:

0.645

AC:

98025

AN:

151928

Hom.:

32711

Cov.:

show subpopulations

Gnomad AFR

AF:

0.826

Gnomad AMI

AF:

0.640

Gnomad AMR

AF:

0.562

Gnomad ASJ

AF:

0.554

Gnomad EAS

AF:

0.472

Gnomad SAS

AF:

0.580

Gnomad FIN

AF:

0.603

Gnomad MID

AF:

0.666

Gnomad NFE

AF:

0.585

Gnomad OTH

AF:

0.592

GnomAD4 exome

AF:

0.660

AC:

AN:

Hom.:

Cov.:

AF XY:

0.667

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.833

Gnomad4 EAS exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.632

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.645

AC:

98133

AN:

152046

Hom.:

32756

Cov.:

AF XY:

0.643

AC XY:

47778

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.826

Gnomad4 AMR

AF:

0.561

Gnomad4 ASJ

AF:

0.554

Gnomad4 EAS

AF:

0.472

Gnomad4 SAS

AF:

0.579

Gnomad4 FIN

AF:

0.603

Gnomad4 NFE

AF:

0.585

Gnomad4 OTH

AF:

0.593

Alfa

AF:

0.519

Hom.:

1577

Bravo

AF:

0.648

Asia WGS

AF:

0.549

AC:

1910

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

2.2

DANN

Benign

0.83

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