rs5742694

Positions:

• chr12-102405458-C-A
• chr12-102405458-C-G
• chr12-102405458-C-T

Variant summary

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

The NM_000618.5(IGF1):​c.403-2892G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 151,746 control chromosomes in the GnomAD database, including 44,629 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 0.77 (44629 hom., cov: 29)
• Consequence: IGF1 NM_000618.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

Genes affected

IGF1 (HGNC:5464): (insulin like growth factor 1) The protein encoded by this gene is similar to insulin in function and structure and is a member of a family of proteins involved in mediating growth and development. The encoded protein is processed from a precursor, bound by a specific receptor, and secreted. Defects in this gene are a cause of insulin-like growth factor I deficiency. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar processing to generate mature protein. [provided by RefSeq, Sep 2015]

LINC02456 (HGNC:53389): (long intergenic non-protein coding RNA 2456)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IGF1	NM_000618.5	c.403-2892G>T		intron_variant		ENST00000337514.11	NP_000609.1
LINC02456	XR_007063427.1	n.815+1227C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IGF1	ENST00000337514.11	c.403-2892G>T		intron_variant		1	NM_000618.5	ENSP00000337612	P1
LINC02456	ENST00000704346.1	n.1067-17613C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116213 AN: 151628 Hom.: 44593 Cov.: 29

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.766 AC: 116300 AN: 151746 Hom.: 44629 Cov.: 29 AF XY: 0.769 AC XY: 56990 AN XY: 74136

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.835

Gnomad4 ASJ AF: 0.738

Gnomad4 EAS AF: 0.830

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.769

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.771

Alfa AF: 0.750 Hom.: 6257

Bravo AF: 0.775

Asia WGS AF: 0.785 AC: 2729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.44

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: rs5742694; hg19: chr12-102799236; COSMIC: COSV61705253; COSMIC: COSV61705253;