15-98727906-A-G

Position:

• chr15-98727906-A-G

Variant summary

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

The NM_000875.5(IGF1R):​c.640+19799A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 151,778 control chromosomes in the GnomAD database, including 25,725 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 0.58 (25725 hom., cov: 30)
• Consequence: IGF1R NM_000875.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640

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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGF1R	NM_000875.5	c.640+19799A>G		intron_variant		ENST00000650285.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IGF1R	ENST00000650285.1	c.640+19799A>G		intron_variant			NM_000875.5	P4
IGF1R	ENST00000559925.5	n.640+19799A>G		intron_variant, non_coding_transcript_variant		1
IGF1R	ENST00000558355.1	c.277+19799A>G		intron_variant		2
IGF1R	ENST00000649865.1	c.640+19799A>G		intron_variant				A1

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87461 AN: 151662 Hom.: 25720 Cov.: 30

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.576 AC: 87476 AN: 151778 Hom.: 25725 Cov.: 30 AF XY: 0.575 AC XY: 42632 AN XY: 74148

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.574

Alfa AF: 0.597 Hom.: 3527

Bravo AF: 0.566

Asia WGS AF: 0.503 AC: 1751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.1
DANN	Benign	0.79

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: rs6598541; hg19: chr15-99271135;