chr3-159887763-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_014575.4(SCHIP1):c.1052C>G(p.Ser351Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,613,902 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000096 ( 0 hom. )
Consequence
SCHIP1
NM_014575.4 missense
NM_014575.4 missense
Scores
2
10
5
Clinical Significance
Conservation
PhyloP100: 7.20
Genes affected
SCHIP1 (HGNC:15678): (schwannomin interacting protein 1) Enables identical protein binding activity. Predicted to be involved in positive regulation of hippo signaling. Predicted to act upstream of or within several processes, including animal organ development; face morphogenesis; and fibroblast migration. Located in several cellular components, including cell junction; cytosol; and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCHIP1 | NM_014575.4 | c.1052C>G | p.Ser351Cys | missense_variant | 5/8 | ENST00000638749.2 | |
IQCJ-SCHIP1 | NM_001197113.2 | c.1280C>G | p.Ser427Cys | missense_variant | 8/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCHIP1 | ENST00000445224.6 | c.323C>G | p.Ser108Cys | missense_variant | 4/7 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251152Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135722
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GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461694Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 727158
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GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74344
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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 | Dec 07, 2021 | The c.1280C>G (p.S427C) alteration is located in exon 8 (coding exon 8) of the IQCJ-SCHIP1 gene. This alteration results from a C to G substitution at nucleotide position 1280, causing the serine (S) at amino acid position 427 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D;D;D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;N;.;N;D;N;D;D
REVEL
Benign
Sift
Uncertain
D;D;.;D;D;D;D;D
Sift4G
Uncertain
D;D;.;D;T;D;T;T
Polyphen
1.0, 0.99
.;.;.;.;.;D;.;D
Vest4
MutPred
0.41
.;.;Gain of glycosylation at S351 (P = 0.0074);.;.;.;.;.;
MVP
MPC
1.0, 0.65
ClinPred
D
GERP RS
Varity_R
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