rs2684777

chr15-98853465-T-Cchr15-98853465-T-G

Variant summary

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

The NM_000875.5(IGF1R):c.641-37860T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,132 control chromosomes in the GnomAD database, including 4,345 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 0.22 (4345 hom., cov: 33)
• Consequence: IGF1R NM_000875.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGF1R	NM_000875.5	c.641-37860T>C		intron_variant		ENST00000650285.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IGF1R	ENST00000650285.1	c.641-37860T>C		intron_variant			NM_000875.5	P4

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33151 AN: 152014 Hom.: 4340 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.218 AC: 33172 AN: 152132 Hom.: 4345 Cov.: 33 AF XY: 0.226 AC XY: 16796 AN XY: 74354

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.230

Alfa AF: 0.219 Hom.: 5318

Bravo AF: 0.212

Asia WGS AF: 0.301 AC: 1047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	13
Dann	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs2684777; hg19: chr15-99396694; COSMIC: COSV51269315;