chr1-116579666-G-C
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_001007237.3(IGSF3):c.3060C>G(p.Asp1020Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 149,828 control chromosomes in the GnomAD database, including 8,974 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001007237.3 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 |
---|---|---|---|---|---|---|---|
IGSF3 | NM_001007237.3 | c.3060C>G | p.Asp1020Glu | missense_variant | 10/11 | ENST00000369486.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGSF3 | ENST00000369486.8 | c.3060C>G | p.Asp1020Glu | missense_variant | 10/11 | 1 | NM_001007237.3 | P4 | |
IGSF3 | ENST00000318837.6 | c.3120C>G | p.Asp1040Glu | missense_variant | 10/11 | 2 | A1 | ||
IGSF3 | ENST00000369483.5 | c.3120C>G | p.Asp1040Glu | missense_variant | 11/12 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.328 AC: 49109AN: 149712Hom.: 8974 Cov.: 28
GnomAD3 exomes AF: 0.325 AC: 69863AN: 215072Hom.: 12044 AF XY: 0.332 AC XY: 38594AN XY: 116374
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.377 AC: 539225AN: 1429598Hom.: 105070 Cov.: 35 AF XY: 0.377 AC XY: 267864AN XY: 710572
GnomAD4 genome ? AF: 0.328 AC: 49116AN: 149828Hom.: 8974 Cov.: 28 AF XY: 0.330 AC XY: 24130AN XY: 73054
ClinVar
Submissions by phenotype
IGSF3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at