9-2029099-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4

The NM_003070.5(SMARCA2):ā€‹c.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

Scores

2
10
7

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.17
Variant links:
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]

Genome browser will be placed here

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
SMARCA2NM_003070.5 linkuse as main transcriptc.77T>C p.Ile26Thr missense_variant 2/34 ENST00000349721.8
SMARCA2NM_001289396.1 linkuse as main transcriptc.77T>C p.Ile26Thr missense_variant 2/34
SMARCA2NM_139045.4 linkuse as main transcriptc.77T>C p.Ile26Thr missense_variant 2/33
SMARCA2NM_001289397.2 linkuse as main transcriptc.77T>C p.Ile26Thr missense_variant 2/33

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SMARCA2ENST00000349721.8 linkuse as main transcriptc.77T>C p.Ile26Thr missense_variant 2/345 NM_003070.5 P2P51531-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000462
AC:
1
AN:
216582
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
117018
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000613
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1439992
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
714408
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000756

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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 16, 2023This 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.79
BayesDel_addAF
Uncertain
0.097
D
BayesDel_noAF
Uncertain
0.080
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Benign
0.029
.;.;T;T;T;T;T;.;T;T;T
Eigen
Uncertain
0.20
Eigen_PC
Uncertain
0.33
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Uncertain
0.95
.;D;.;.;.;D;D;D;D;D;D
M_CAP
Benign
0.048
D
MetaRNN
Benign
0.35
T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Uncertain
0.038
D
MutationAssessor
Benign
1.7
L;.;.;L;.;.;.;L;.;.;L
MutationTaster
Benign
1.0
D;D;D;D
PrimateAI
Pathogenic
0.90
D
PROVEAN
Benign
-0.56
N;N;.;N;.;.;D;N;D;.;N
REVEL
Uncertain
0.46
Sift
Uncertain
0.0040
D;D;.;D;.;.;D;D;D;.;D
Sift4G
Benign
0.20
T;T;.;T;.;.;T;T;T;.;T
Polyphen
0.56
P;.;.;B;.;.;.;P;.;.;B
Vest4
0.49
MutPred
0.27
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
0.65
MPC
0.056
ClinPred
0.41
T
GERP RS
5.8
Varity_R
0.27
gMVP
0.041

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1184325506; hg19: chr9-2029099; API