NM_000875.5:c.-33delT

Variant names:

• chr15-98649525-CT-C
• rs544674838
• NM_000875.5:c.-33delT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_000875.5(IGF1R):​c.-33delT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.013 (4 hom., cov: 0)
  • Exomes 𝑓: 0.011 (0 hom.)
• Consequence: IGF1R NM_000875.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

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.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0128 (1590/124420) while in subpopulation AFR AF= 0.0277 (931/33592). AF 95% confidence interval is 0.0262. There are 4 homozygotes in gnomad4. There are 720 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 4 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGF1R	NM_000875.5	c.-33delT		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.-33delT		5_prime_UTR_variant	Exon 1 of 21		NM_000875.5	ENSP00000497069.1
IGF1R	ENST00000649865	c.-33delT		5_prime_UTR_variant	Exon 1 of 21			ENSP00000496919.1
IGF1R	ENST00000559925.5	n.-56delT		upstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.0128 AC: 1587 AN: 124410 Hom.: 4 Cov.: 0

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.0364

Gnomad AMR AF: 0.00779

Gnomad ASJ AF: 0.00791

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.0200

Gnomad FIN AF: 0.000889

Gnomad MID AF: 0.0132

Gnomad NFE AF: 0.00598

Gnomad OTH AF: 0.0144

GnomAD4 exome AF: 0.0107 AC: 6340 AN: 594748 Hom.: 0 Cov.: 0 AF XY: 0.0106 AC XY: 3367 AN XY: 317374

Gnomad4 AFR exome AF: 0.0110

Gnomad4 AMR exome AF: 0.00797

Gnomad4 ASJ exome AF: 0.0133

Gnomad4 EAS exome AF: 0.0310

Gnomad4 SAS exome AF: 0.00493

Gnomad4 FIN exome AF: 0.0103

Gnomad4 NFE exome AF: 0.00997

Gnomad4 OTH exome AF: 0.0130

GnomAD4 genome AF: 0.0128 AC: 1590 AN: 124420 Hom.: 4 Cov.: 0 AF XY: 0.0121 AC XY: 720 AN XY: 59400

Gnomad4 AFR AF: 0.0277

Gnomad4 AMR AF: 0.00778

Gnomad4 ASJ AF: 0.00791

Gnomad4 EAS AF: 0.0112

Gnomad4 SAS AF: 0.0201

Gnomad4 FIN AF: 0.000889

Gnomad4 NFE AF: 0.00598

Gnomad4 OTH AF: 0.0143

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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;