9-2029099-T-C
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_003070.5(SMARCA2):āc.77T>Cā(p.Ile26Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 33)
Exomes š: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SMARCA2
NM_003070.5 missense
NM_003070.5 missense
Scores
2
10
7
Clinical Significance
Conservation
PhyloP100: 6.17
Genes affected
SMARCA2 (HGNC:11098): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2) The protein encoded by this gene is a member of the SWI/SNF family of proteins and is highly similar to the brahma protein of Drosophila. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which is required for transcriptional activation of genes normally repressed by chromatin. Alternatively spliced transcript variants encoding different isoforms have been found for this gene, which contains a trinucleotide repeat (CAG) length polymorphism. [provided by RefSeq, Jan 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), SMARCA2. . Gene score misZ 5.054 (greater than the threshold 3.09). Trascript score misZ 4.663 (greater than threshold 3.09). GenCC has associacion of gene with intellectual disability-sparse hair-brachydactyly syndrome, Coffin-Siris syndrome 1.
BP4
Computational evidence support a benign effect (MetaRNN=0.3491689).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCA2 | NM_003070.5 | c.77T>C | p.Ile26Thr | missense_variant | 2/34 | ENST00000349721.8 | |
SMARCA2 | NM_001289396.1 | c.77T>C | p.Ile26Thr | missense_variant | 2/34 | ||
SMARCA2 | NM_139045.4 | c.77T>C | p.Ile26Thr | missense_variant | 2/33 | ||
SMARCA2 | NM_001289397.2 | c.77T>C | p.Ile26Thr | missense_variant | 2/33 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCA2 | ENST00000349721.8 | c.77T>C | p.Ile26Thr | missense_variant | 2/34 | 5 | NM_003070.5 | P2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
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33
GnomAD3 exomes AF: 0.00000462 AC: 1AN: 216582Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 117018
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1439992Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 714408
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GnomAD4 genome Cov.: 33
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33
Bravo
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 16, 2023 | This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 26 of the SMARCA2 protein (p.Ile26Thr). This variant is present in population databases (no rsID available, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with SMARCA2-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SMARCA2 protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;.;T;T;T;T;T;.;T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;D;.;.;.;D;D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Benign
L;.;.;L;.;.;.;L;.;.;L
MutationTaster
Benign
D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;.;N;.;.;D;N;D;.;N
REVEL
Uncertain
Sift
Uncertain
D;D;.;D;.;.;D;D;D;.;D
Sift4G
Benign
T;T;.;T;.;.;T;T;T;.;T
Polyphen
P;.;.;B;.;.;.;P;.;.;B
Vest4
MutPred
Gain of glycosylation at I26 (P = 4e-04);Gain of glycosylation at I26 (P = 4e-04);Gain of glycosylation at I26 (P = 4e-04);Gain of glycosylation at I26 (P = 4e-04);Gain of glycosylation at I26 (P = 4e-04);Gain of glycosylation at I26 (P = 4e-04);Gain of glycosylation at I26 (P = 4e-04);Gain of glycosylation at I26 (P = 4e-04);Gain of glycosylation at I26 (P = 4e-04);Gain of glycosylation at I26 (P = 4e-04);Gain of glycosylation at I26 (P = 4e-04);
MVP
MPC
0.056
ClinPred
T
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