7-45916597-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000598.5(IGFBP3):c.701G>A(p.Gly234Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,360 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G234S) has been classified as Benign.
Frequency
Consequence
NM_000598.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IGFBP3 | NM_000598.5 | c.701G>A | p.Gly234Asp | missense_variant | Exon 3 of 5 | ENST00000613132.5 | NP_000589.2 | |
IGFBP3 | NM_001013398.2 | c.719G>A | p.Gly240Asp | missense_variant | Exon 3 of 5 | NP_001013416.1 | ||
IGFBP3 | XM_047420325.1 | c.701G>A | p.Gly234Asp | missense_variant | Exon 3 of 4 | XP_047276281.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251480Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135912
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461084Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 726816
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.719G>A (p.G240D) alteration is located in exon 3 (coding exon 3) of the IGFBP3 gene. This alteration results from a G to A substitution at nucleotide position 719, causing the glycine (G) at amino acid position 240 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at