15-98649525-CTTTTTTTTTTTTTTTTTTTT-CTTTTTTTTTTTT

Variant names:

• chr15-98649525-CTTTTTTTT-C
• rs544674838
• NM_000875.5:c.-40_-33delTTTTTTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000875.5(IGF1R):​c.-40_-33delTTTTTTTT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 708,360 control chromosomes in the GnomAD database, including 4,427 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.20 (3158 hom., cov: 0)
  • Exomes 𝑓: 0.13 (1269 hom.)
• Consequence: IGF1R NM_000875.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58

Genes affected

IGF1R (HGNC:5465): (insulin like growth factor 1 receptor) This receptor binds insulin-like growth factor with a high affinity. It has tyrosine kinase activity. The insulin-like growth factor I receptor plays a critical role in transformation events. Cleavage of the precursor generates alpha and beta subunits. It is highly overexpressed in most malignant tissues where it functions as an anti-apoptotic agent by enhancing cell survival. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, May 2014]

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGF1R	NM_000875.5	c.-40_-33delTTTTTTTT		5_prime_UTR_variant	Exon 1 of 21	ENST00000650285.1	NP_000866.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IGF1R	ENST00000650285	c.-40_-33delTTTTTTTT		5_prime_UTR_variant	Exon 1 of 21		NM_000875.5	ENSP00000497069.1
IGF1R	ENST00000649865	c.-40_-33delTTTTTTTT		5_prime_UTR_variant	Exon 1 of 21			ENSP00000496919.1
IGF1R	ENST00000559925.5	n.-56_-49delTTTTTTTT		upstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.200 AC: 25007 AN: 124748 Hom.: 3158 Cov.: 0

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.00373

Gnomad SAS AF: 0.0842

Gnomad FIN AF: 0.0391

Gnomad MID AF: 0.254

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.189

GnomAD4 exome AF: 0.134 AC: 78050 AN: 583604 Hom.: 1269 AF XY: 0.131 AC XY: 40630 AN XY: 310808

Gnomad4 AFR exome AF: 0.313

Gnomad4 AMR exome AF: 0.0934

Gnomad4 ASJ exome AF: 0.170

Gnomad4 EAS exome AF: 0.0316

Gnomad4 SAS exome AF: 0.0785

Gnomad4 FIN exome AF: 0.0666

Gnomad4 NFE exome AF: 0.147

Gnomad4 OTH exome AF: 0.150

GnomAD4 genome AF: 0.201 AC: 25018 AN: 124756 Hom.: 3158 Cov.: 0 AF XY: 0.193 AC XY: 11524 AN XY: 59576

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.00374

Gnomad4 SAS AF: 0.0842

Gnomad4 FIN AF: 0.0391

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.187

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs544674838; hg19: chr15-99192754;