11-2133089-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_000612.6(IGF2):c.441G>A(p.Glu147=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000796 in 1,608,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000079 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000080 ( 0 hom. )
Consequence
IGF2
NM_000612.6 synonymous
NM_000612.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.704
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 11-2133089-C-T is Benign according to our data. Variant chr11-2133089-C-T is described in ClinVar as [Benign]. Clinvar id is 1598735.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.704 with no splicing effect.
BS2
?
High AC in GnomAd at 12 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGF2 | NM_000612.6 | c.441G>A | p.Glu147= | synonymous_variant | 4/4 | ENST00000416167.7 | |
INS-IGF2 | NR_003512.4 | n.1155G>A | non_coding_transcript_exon_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGF2 | ENST00000416167.7 | c.441G>A | p.Glu147= | synonymous_variant | 4/4 | 1 | NM_000612.6 | P4 | |
ENST00000643349.2 | c.*493G>A | 3_prime_UTR_variant | 5/5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152220Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000115 AC: 28AN: 244300Hom.: 0 AF XY: 0.000128 AC XY: 17AN XY: 132824
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GnomAD4 exome AF: 0.0000797 AC: 116AN: 1455800Hom.: 0 Cov.: 31 AF XY: 0.0000719 AC XY: 52AN XY: 723618
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GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74386
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 30, 2023 | - - |
Computational scores
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Benign
Cadd
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at