chr12-102407157-C-T

Variant names:

• chr12-102407157-C-T
• rs6539035
• NM_000618.5:c.403-4591G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000618.5(IGF1):​c.403-4591G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 142,272 control chromosomes in the GnomAD database, including 42,727 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 0.78 (42727 hom., cov: 24)
• Consequence: IGF1 NM_000618.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000618.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGF1	NM_000618.5	MANE Select	c.403-4591G>A		intron	N/A	NP_000609.1	Q5U743
	IGF1	NM_001111283.3		c.452-4591G>A		intron	N/A	NP_001104753.1	P05019-4
	IGF1	NM_001414007.1		c.403-4591G>A		intron	N/A	NP_001400936.1	Q5U743

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGF1	ENST00000337514.11	TSL:1 MANE Select	c.403-4591G>A		intron	N/A	ENSP00000337612.7	P05019-2
	IGF1	ENST00000424202.6	TSL:1	c.355-4591G>A		intron	N/A	ENSP00000416811.2	P05019-3
	IGF1	ENST00000392904.5	TSL:5	c.452-4591G>A		intron	N/A	ENSP00000376637.1	P05019-4

Frequencies

GnomAD3 genomes AF: 0.783 AC: 111379 AN: 142196 Hom.: 42702 Cov.: 24

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.783 AC: 111440 AN: 142272 Hom.: 42727 Cov.: 24 AF XY: 0.787 AC XY: 54184 AN XY: 68866

African (AFR) AF: 0.779 AC: 29719 AN: 38162

American (AMR) AF: 0.849 AC: 12214 AN: 14392

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2539 AN: 3330

East Asian (EAS) AF: 0.846 AC: 4078 AN: 4818

South Asian (SAS) AF: 0.768 AC: 3428 AN: 4466

European-Finnish (FIN) AF: 0.799 AC: 6905 AN: 8644

Middle Eastern (MID) AF: 0.746 AC: 206 AN: 276

European-Non Finnish (NFE) AF: 0.765 AC: 49978 AN: 65314

Other (OTH) AF: 0.788 AC: 1553 AN: 1972

Alfa AF: 0.756 Hom.: 7403

Bravo AF: 0.771

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.78
DANN	Benign	0.22
PhyloP100		-0.47
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6539035; hg19: chr12-102800935;