rs1003483
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000643349.2(ENSG00000284779):c.*46+1253A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 535,818 control chromosomes in the GnomAD database, including 58,442 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 0.40 ( 13961 hom., cov: 34)
Exomes 𝑓: 0.47 ( 44481 hom. )
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.02
Genes affected
IGF2-AS (HGNC:14062): (IGF2 antisense RNA) This gene is expressed in antisense to the insulin-like growth factor 2 (IGF2) gene and is imprinted and paternally expressed. It is thought to be non-coding because the putative protein is not conserved and translation is predicted to trigger nonsense mediated decay (NMD). Transcripts from this gene are produced in tumors and may function to suppress cell growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2015]
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGF2-AS | NR_028043.2 | n.505T>G | non_coding_transcript_exon_variant | 2/3 | |||
INS-IGF2 | NR_003512.4 | n.708+1253A>C | intron_variant, non_coding_transcript_variant | ||||
IGF2 | NM_001007139.6 | c.-7+1253A>C | intron_variant | ||||
IGF2-AS | NR_133657.1 | n.437-43T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000643349.2 | c.*46+1253A>C | intron_variant | P1 | ||||||
IGF2-AS | ENST00000381361.4 | n.500T>G | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.399 AC: 60682AN: 152048Hom.: 13946 Cov.: 34
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GnomAD3 exomes AF: 0.465 AC: 115517AN: 248336Hom.: 28789 AF XY: 0.459 AC XY: 61951AN XY: 134876
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GnomAD4 exome AF: 0.469 AC: 180029AN: 383652Hom.: 44481 Cov.: 0 AF XY: 0.459 AC XY: 100368AN XY: 218456
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GnomAD4 genome ? AF: 0.399 AC: 60714AN: 152166Hom.: 13961 Cov.: 34 AF XY: 0.405 AC XY: 30143AN XY: 74392
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at