chr15-78437910-A-G

Position:

• chr15-78437910-A-G

Variant summary

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

The NM_001354994.2(IREB2):​c.-153+189A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 152,196 control chromosomes in the GnomAD database, including 46,559 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 0.78 (46559 hom., cov: 33)
• Consequence: IREB2 NM_001354994.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.34

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IREB2	NM_001354994.2	c.-153+189A>G		intron_variant			NP_001341923.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IREB2	ENST00000560840.5	c.-153+189A>G		intron_variant		5		ENSP00000453172

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118523 AN: 152078 Hom.: 46504 Cov.: 33

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.779 AC: 118632 AN: 152196 Hom.: 46559 Cov.: 33 AF XY: 0.775 AC XY: 57629 AN XY: 74380

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.762

Alfa AF: 0.777 Hom.: 10184

Bravo AF: 0.779

Asia WGS AF: 0.665 AC: 2315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.42
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2656070; hg19: chr15-78730252;