rs4074555
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_034081.1(IGFBP7-AS1):n.209+430C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,249,564 control chromosomes in the GnomAD database, including 9,567 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 0.15 ( 2500 hom., cov: 32)
Exomes 𝑓: 0.096 ( 7067 hom. )
Consequence
IGFBP7-AS1
NR_034081.1 intron, non_coding_transcript
NR_034081.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -5.96
Genes affected
IGFBP7-AS1 (HGNC:40296): (IGFBP7 antisense RNA 1)
IGFBP7 (HGNC:5476): (insulin like growth factor binding protein 7) This gene encodes a member of the insulin-like growth factor (IGF)-binding protein (IGFBP) family. IGFBPs bind IGFs with high affinity, and regulate IGF availability in body fluids and tissues and modulate IGF binding to its receptors. This protein binds IGF-I and IGF-II with relatively low affinity, and belongs to a subfamily of low-affinity IGFBPs. It also stimulates prostacyclin production and cell adhesion. Alternatively spliced transcript variants encoding different isoforms have been described for this gene, and one variant has been associated with retinal arterial macroaneurysm (PMID:21835307). [provided by RefSeq, Dec 2011]
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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=-0.78).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGFBP7-AS1 | NR_034081.1 | n.209+430C>A | intron_variant, non_coding_transcript_variant | ||||
IGFBP7 | NM_001553.3 | upstream_gene_variant | ENST00000295666.6 | ||||
IGFBP7 | NM_001253835.2 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGFBP7-AS1 | ENST00000499667.6 | n.209+430C>A | intron_variant, non_coding_transcript_variant | 1 | |||||
IGFBP7-AS1 | ENST00000508328.6 | n.191+430C>A | intron_variant, non_coding_transcript_variant | 3 | |||||
IGFBP7 | ENST00000295666.6 | upstream_gene_variant | 1 | NM_001553.3 | P2 | ||||
IGFBP7 | ENST00000514062.2 | upstream_gene_variant | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.153 AC: 23200AN: 151194Hom.: 2501 Cov.: 32
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GnomAD3 exomes AF: 0.374 AC: 119AN: 318Hom.: 22 AF XY: 0.342 AC XY: 69AN XY: 202
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GnomAD4 exome AF: 0.0956 AC: 105000AN: 1098262Hom.: 7067 Cov.: 31 AF XY: 0.0959 AC XY: 50335AN XY: 524888
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GnomAD4 genome ? AF: 0.154 AC: 23226AN: 151302Hom.: 2500 Cov.: 32 AF XY: 0.154 AC XY: 11360AN XY: 73942
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ClinVar
Not reported inComputational scores
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Name
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Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at