rs5742629

Positions:

• chr12-102463485-T-C

Variant summary

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

The NM_000618.5(IGF1):​c.220+12158A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,998 control chromosomes in the GnomAD database, including 8,022 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 0.32 (8021 hom., cov: 32)
  • Exomes 𝑓: 0.33 (1 hom.)
• Consequence: IGF1 NM_000618.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGF1	NM_000618.5	c.220+12158A>G		intron_variant		ENST00000337514.11
LINC02456	XR_007063427.1	n.14499T>C		non_coding_transcript_exon_variant	11/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IGF1	ENST00000337514.11	c.220+12158A>G		intron_variant		1	NM_000618.5	P1
LINC02456	ENST00000704346.1	n.1934T>C		non_coding_transcript_exon_variant	11/11

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48176 AN: 151874 Hom.: 7991 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.290

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.318 AC: 48270 AN: 151992 Hom.: 8021 Cov.: 32 AF XY: 0.318 AC XY: 23639 AN XY: 74284

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.296

Alfa AF: 0.284 Hom.: 2928

Bravo AF: 0.314

Asia WGS AF: 0.412 AC: 1431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.78

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: rs5742629; hg19: chr12-102857263;