rs2289965
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173588.4(IGSF22):āc.3391A>Gā(p.Ile1131Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 1,551,224 control chromosomes in the GnomAD database, including 105,711 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_173588.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IGSF22 | NM_173588.4 | c.3391A>G | p.Ile1131Val | missense_variant | Exon 21 of 23 | ENST00000513874.6 | NP_775859.4 | |
IGSF22 | XM_047426830.1 | c.1465A>G | p.Ile489Val | missense_variant | Exon 8 of 10 | XP_047282786.1 | ||
IGSF22 | NR_160413.1 | n.3147A>G | non_coding_transcript_exon_variant | Exon 19 of 21 | ||||
IGSF22-AS1 | NR_186353.1 | n.623T>C | non_coding_transcript_exon_variant | Exon 1 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.284 AC: 43134AN: 151984Hom.: 7851 Cov.: 32
GnomAD3 exomes AF: 0.325 AC: 50029AN: 153960Hom.: 9089 AF XY: 0.321 AC XY: 26192AN XY: 81674
GnomAD4 exome AF: 0.365 AC: 510842AN: 1399122Hom.: 97857 Cov.: 41 AF XY: 0.361 AC XY: 249363AN XY: 690090
GnomAD4 genome AF: 0.284 AC: 43140AN: 152102Hom.: 7854 Cov.: 32 AF XY: 0.290 AC XY: 21548AN XY: 74344
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at