rs61740877
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_000875.5(IGF1R):c.1474G>A(p.Val492Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000409 in 1,614,068 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000875.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGF1R | NM_000875.5 | c.1474G>A | p.Val492Ile | missense_variant | 7/21 | ENST00000650285.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGF1R | ENST00000650285.1 | c.1474G>A | p.Val492Ile | missense_variant | 7/21 | NM_000875.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00220 AC: 335AN: 152086Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.000569 AC: 143AN: 251440Hom.: 0 AF XY: 0.000390 AC XY: 53AN XY: 135894
GnomAD4 exome AF: 0.000223 AC: 326AN: 1461864Hom.: 2 Cov.: 32 AF XY: 0.000193 AC XY: 140AN XY: 727238
GnomAD4 genome AF: 0.00219 AC: 334AN: 152204Hom.: 5 Cov.: 32 AF XY: 0.00207 AC XY: 154AN XY: 74414
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 30, 2014 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at