11-18705953-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_173588.4(IGSF22):āc.3774G>Cā(p.Lys1258Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000999 in 1,551,640 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_173588.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IGSF22 | NM_173588.4 | c.3774G>C | p.Lys1258Asn | missense_variant | 22/23 | ENST00000513874.6 | NP_775859.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IGSF22 | ENST00000513874.6 | c.3774G>C | p.Lys1258Asn | missense_variant | 22/23 | 5 | NM_173588.4 | ENSP00000421191 | P1 | |
IGSF22 | ENST00000510673.1 | n.177G>C | non_coding_transcript_exon_variant | 1/2 | 3 | |||||
IGSF22 | ENST00000319338.6 | c.*670G>C | 3_prime_UTR_variant, NMD_transcript_variant | 20/21 | 2 | ENSP00000322422 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152238Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000843 AC: 13AN: 154120Hom.: 0 AF XY: 0.0000856 AC XY: 7AN XY: 81786
GnomAD4 exome AF: 0.0000950 AC: 133AN: 1399402Hom.: 0 Cov.: 32 AF XY: 0.0000840 AC XY: 58AN XY: 690214
GnomAD4 genome AF: 0.000145 AC: 22AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 06, 2022 | The c.3774G>C (p.K1258N) alteration is located in exon 22 (coding exon 21) of the IGSF22 gene. This alteration results from a G to C substitution at nucleotide position 3774, causing the lysine (K) at amino acid position 1258 to be replaced by an asparagine (N). 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