rs1140655

chr12-102397002-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000618.5(IGF1):c.*5505T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 394,082 control chromosomes in the GnomAD database, including 89,252 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.65 (32917 hom., cov: 29)
  • Exomes 𝑓: 0.68 (56335 hom.)
• Consequence: IGF1 NM_000618.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.836

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]

HELLPAR (HGNC:43984): (HELLP associated long non-coding RNA)

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

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 12-102397002-A-T is Benign according to our data. Variant chr12-102397002-A-T is described in ClinVar as [Benign]. Clinvar id is 306840.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGF1	NM_000618.5	c.*5505T>A		3_prime_UTR_variant	4/4	ENST00000337514.11
LINC02456	XR_007063427.1	n.697-7111A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IGF1	ENST00000337514.11	c.*5505T>A		3_prime_UTR_variant	4/4	1	NM_000618.5	P1
HELLPAR	ENST00000626826.1	n.199418A>T		non_coding_transcript_exon_variant	1/1
LINC02456	ENST00000704346.1	n.1067-26069A>T		intron_variant, non_coding_transcript_variant
LINC02456	ENST00000635615.1	n.450-26069A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99278 AN: 151652 Hom.: 32912 Cov.: 29

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.635

GnomAD4 exome AF: 0.678 AC: 164310 AN: 242312 Hom.: 56335 Cov.: 0 AF XY: 0.678 AC XY: 83362 AN XY: 122872

Gnomad4 AFR exome AF: 0.554

Gnomad4 AMR exome AF: 0.660

Gnomad4 ASJ exome AF: 0.649

Gnomad4 EAS exome AF: 0.512

Gnomad4 SAS exome AF: 0.705

Gnomad4 FIN exome AF: 0.776

Gnomad4 NFE exome AF: 0.700

Gnomad4 OTH exome AF: 0.657

GnomAD4 genome AF: 0.654 AC: 99316 AN: 151770 Hom.: 32917 Cov.: 29 AF XY: 0.658 AC XY: 48762 AN XY: 74156

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.630

Alfa AF: 0.680 Hom.: 4433

Bravo AF: 0.636

Asia WGS AF: 0.575 AC: 2001 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Growth delay due to insulin-like growth factor type 1 deficiency Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.81
Dann	Benign	0.80

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: rs1140655; hg19: chr12-102790780;