chr15-98956835-C-T

Position:

• chr15-98956835-C-T

Variant summary

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

The NM_000875.5(IGF1R):​c.3723-226C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,084 control chromosomes in the GnomAD database, including 3,028 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 0.19 (3028 hom., cov: 33)
• Consequence: IGF1R NM_000875.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

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]

SYNM-AS1 (HGNC:55421): (SYNM antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGF1R	NM_000875.5	c.3723-226C>T		intron_variant		ENST00000650285.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IGF1R	ENST00000650285.1	c.3723-226C>T		intron_variant			NM_000875.5	P4
SYNM-AS1	ENST00000559468.1	n.349-2447G>A		intron_variant, non_coding_transcript_variant		4
IGF1R	ENST00000649865.1	c.3720-226C>T		intron_variant				A1
IGF1R	ENST00000558751.1	n.317-226C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28707 AN: 151966 Hom.: 3025 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0540

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.189 AC: 28725 AN: 152084 Hom.: 3028 Cov.: 33 AF XY: 0.185 AC XY: 13785 AN XY: 74332

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.0537

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.169

Alfa AF: 0.206 Hom.: 2001

Bravo AF: 0.182

Asia WGS AF: 0.108 AC: 377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.49

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: rs12440962; hg19: chr15-99500064;