11-2133027-T-G

Variant names:

• chr11-2133027-T-G
• NM_000612.6:c.503A>C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_000612.6(IGF2):​c.503A>C​(p.His168Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: IGF2 NM_000612.6 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.737

Genes affected

IGF2 (HGNC:5466): (insulin like growth factor 2) This gene encodes a member of the insulin family of polypeptide growth factors, which are involved in development and growth. It is an imprinted gene, expressed only from the paternal allele, and epigenetic changes at this locus are associated with Wilms tumour, Beckwith-Wiedemann syndrome, rhabdomyosarcoma, and Silver-Russell syndrome. A read-through INS-IGF2 gene exists, whose 5' region overlaps the INS gene and the 3' region overlaps this gene. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2010]

ENSG00000284779 (HGNC:):

INS-IGF2 (HGNC:33527): (INS-IGF2 readthrough) This locus includes two alternatively spliced read-through transcript variants which align to the INS gene in the 5' region and to the IGF2 gene in the 3' region. One transcript is predicted to encode a protein which shares the N-terminus with the INS protein but has a distinct and longer C-terminus, whereas the other transcript is a candidate for nonsense-mediated decay (NMD). The transcripts are imprinted and are paternally expressed in the limb and eye. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.3350923).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGF2	NM_000612.6	c.503A>C	p.His168Pro	missense_variant	Exon 4 of 4	ENST00000416167.7	NP_000603.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IGF2	ENST00000416167.7	c.503A>C	p.His168Pro	missense_variant	Exon 4 of 4	1	NM_000612.6	ENSP00000414497.2
IGF2	ENST00000381392.5	c.512A>C	p.His171Pro	missense_variant	Exon 4 of 4	1		ENSP00000370799.1
IGF2	ENST00000381406.8	c.512A>C	p.His171Pro	missense_variant	Exon 4 of 4	2		ENSP00000370813.4
ENSG00000284779	ENST00000643349	c.*510A>C		3_prime_UTR_variant	Exon 5 of 5			ENSP00000495715.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Inborn genetic diseases Uncertain:1

Jun 30, 2021

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.671A>C (p.H224P) alteration is located in exon 5 (coding exon 4) of the IGF2 gene. This alteration results from a A to C substitution at nucleotide position 671, causing the histidine (H) at amino acid position 224 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.067
BayesDel_addAF	Uncertain	0.062	T
BayesDel_noAF	Benign	-0.15
CADD	Benign	20
DANN	Benign	0.93
DEOGEN2	Benign	0.39	T;.;T;T;.;.;T;T
Eigen	Benign	-0.039
Eigen_PC	Benign	-0.11
FATHMM_MKL	Benign	0.53	D
LIST_S2	Benign	0.47	.;.;.;.;T;T;.;T
M_CAP	Pathogenic	0.42	D
MetaRNN	Benign	0.34	T;T;T;T;T;T;T;T
MetaSVM	Uncertain	0.071	D
MutationAssessor	Uncertain	2.6	M;.;M;M;.;.;M;M
PrimateAI	Benign	0.33	T
PROVEAN	Uncertain	-2.4	N;N;N;.;D;N;N;N
REVEL	Uncertain	0.35
Sift	Uncertain	0.010	D;D;D;.;D;D;D;D
Sift4G	Benign	0.11	T;T;T;.;D;T;T;T
Polyphen		0.93	P;.;P;P;.;.;P;P
Vest4		0.31
MutPred		0.11		Gain of glycosylation at H168 (P = 0.0469);.;Gain of glycosylation at H168 (P = 0.0469);Gain of glycosylation at H168 (P = 0.0469);.;.;Gain of glycosylation at H168 (P = 0.0469);Gain of glycosylation at H168 (P = 0.0469);
MVP		0.95
MPC		1.9
ClinPred		0.72	D
GERP RS		1.9
Varity_R		0.44
gMVP		0.42

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-2154257;