chr2-226795800-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_005544.3(IRS1):c.2939G>A(p.Arg980Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,460,712 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005544.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRS1 | NM_005544.3 | c.2939G>A | p.Arg980Gln | missense_variant | 1/2 | ENST00000305123.6 | |
IRS1 | XM_047444223.1 | c.2939G>A | p.Arg980Gln | missense_variant | 1/2 | ||
IRS1 | XM_047444224.1 | c.2939G>A | p.Arg980Gln | missense_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRS1 | ENST00000305123.6 | c.2939G>A | p.Arg980Gln | missense_variant | 1/2 | 1 | NM_005544.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249854Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135528
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1460712Hom.: 0 Cov.: 42 AF XY: 0.00000963 AC XY: 7AN XY: 726610
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.2939G>A (p.R980Q) alteration is located in exon 1 (coding exon 1) of the IRS1 gene. This alteration results from a G to A substitution at nucleotide position 2939, causing the arginine (R) at amino acid position 980 to be replaced by a glutamine (Q). 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