chr15-98647372-G-A

Variant names:

• chr15-98647372-G-A
• rs8034564
• ENST00000687383.2:n.138C>T

Variant summary

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

The ENST00000687383.2(IRAIN):​n.138C>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 ENST00000687383.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 6 publications found

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]

ENSG00000278022 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687383.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IRAIN	NR_126453.2		n.3416C>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IRAIN	ENST00000687383.2		n.138C>T		non_coding_transcript_exon	Exon 1 of 1
	IRAIN	ENST00000692203.2		n.74C>T		non_coding_transcript_exon	Exon 1 of 2
	IRAIN	ENST00000747123.1		n.63C>T		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98025 AN: 151928 Hom.: 32711 Cov.: 32

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: 33 AN: 50 Hom.: 10 Cov.: 0 AF XY: 0.667 AC XY: 24 AN XY: 36

African (AFR) AF: 0.833 AC: 5 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.632 AC: 24 AN: 38

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.645 AC: 98133 AN: 152046 Hom.: 32756 Cov.: 32 AF XY: 0.643 AC XY: 47778 AN XY: 74332

African (AFR) AF: 0.826 AC: 34306 AN: 41526

American (AMR) AF: 0.561 AC: 8577 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1921 AN: 3470

East Asian (EAS) AF: 0.472 AC: 2423 AN: 5132

South Asian (SAS) AF: 0.579 AC: 2791 AN: 4824

European-Finnish (FIN) AF: 0.603 AC: 6372 AN: 10574

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.585 AC: 39709 AN: 67922

Other (OTH) AF: 0.593 AC: 1253 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.2
DANN	Benign	0.83
PhyloP100		-0.023

Splicing

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

Other links and lift over

dbSNP: rs8034564; hg19: chr15-99190601;