chr11-18706090-G-T
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_173588.4(IGSF22):c.3637C>A(p.Pro1213Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,548,614 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000016 ( 0 hom. )
Consequence
IGSF22
NM_173588.4 missense
NM_173588.4 missense
Scores
2
6
8
Clinical Significance
Conservation
PhyloP100: 2.31
Genes affected
IGSF22 (HGNC:26750): (immunoglobulin superfamily member 22)
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2632882).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IGSF22 | NM_173588.4 | c.3637C>A | p.Pro1213Thr | 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.3637C>A | p.Pro1213Thr | missense_variant | 22/23 | 5 | NM_173588.4 | ENSP00000421191 | P1 | |
IGSF22 | ENST00000510673.1 | n.40C>A | non_coding_transcript_exon_variant | 1/2 | 3 | |||||
IGSF22 | ENST00000319338.6 | c.*533C>A | 3_prime_UTR_variant, NMD_transcript_variant | 20/21 | 2 | ENSP00000322422 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152224Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000106 AC: 16AN: 150276Hom.: 0 AF XY: 0.000125 AC XY: 10AN XY: 80102
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GnomAD4 exome AF: 0.0000158 AC: 22AN: 1396274Hom.: 0 Cov.: 32 AF XY: 0.0000189 AC XY: 13AN XY: 688930
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152340Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74494
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2023 | The c.3637C>A (p.P1213T) alteration is located in exon 22 (coding exon 21) of the IGSF22 gene. This alteration results from a C to A substitution at nucleotide position 3637, causing the proline (P) at amino acid position 1213 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
M_CAP
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Uncertain
D
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Pathogenic
D
Vest4
MutPred
Gain of phosphorylation at P1213 (P = 0.0238);
MVP
MPC
ClinPred
T
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at