chr1-116579745-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_001007237.3(IGSF3):c.2981G>A(p.Arg994Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001007237.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGSF3 | NM_001007237.3 | c.2981G>A | p.Arg994Lys | missense_variant | 10/11 | ENST00000369486.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGSF3 | ENST00000369486.8 | c.2981G>A | p.Arg994Lys | missense_variant | 10/11 | 1 | NM_001007237.3 | P4 | |
IGSF3 | ENST00000318837.6 | c.3041G>A | p.Arg1014Lys | missense_variant | 10/11 | 2 | A1 | ||
IGSF3 | ENST00000369483.5 | c.3041G>A | p.Arg1014Lys | missense_variant | 11/12 | 5 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 34
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 14, 2022 | The c.3041G>A (p.R1014K) alteration is located in exon 11 (coding exon 10) of the IGSF3 gene. This alteration results from a G to A substitution at nucleotide position 3041, causing the arginine (R) at amino acid position 1014 to be replaced by a lysine (K). 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
Publications
No publications associated with this variant yet.