rs17483548

chr15-78437971-G-Achr15-78437971-G-C

Variant summary

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

The NM_001354994.2(IREB2):c.-153+250G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,190 control chromosomes in the GnomAD database, including 5,431 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 0.23 (5431 hom., cov: 33)
• Consequence: IREB2 NM_001354994.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424

Genes affected

IREB2 (HGNC:6115): (iron responsive element binding protein 2) The protein encoded by this gene is an RNA-binding protein that acts to regulate iron levels in the cells by regulating the translation and stability of mRNAs that affect iron homeostasis under conditions when iron is depleted. When iron levels are low, this protein binds to iron-responsive elements (IRES), stem-loop structures located either in the 5' or 3' UTRs. Binding to the 5' UTR represses translation, while binding to the 3' UTR inhibits mRNA degradation. When iron is found in the cell, this protein is degraded in a F-box and leucine rich repeat protein 5-dependent manner. Variants in this gene have been associated with lung cancer and chronic obstructive pulmonary disease (COPD). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IREB2	NM_001354994.2	c.-153+250G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IREB2	ENST00000560840.5	c.-153+250G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35682 AN: 152072 Hom.: 5429 Cov.: 33

Gnomad AFR AF: 0.0596

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.0398

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.257

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.235 AC: 35691 AN: 152190 Hom.: 5431 Cov.: 33 AF XY: 0.232 AC XY: 17259 AN XY: 74390

Gnomad4 AFR AF: 0.0595

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.0400

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.256

Alfa AF: 0.241 Hom.: 1280

Bravo AF: 0.219

Asia WGS AF: 0.126 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
Cadd	Benign	2.3
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17483548; hg19: chr15-78730313;