9-2029053-C-A

Position:

• chr9-2029053-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2 PP2 BP4

The NM_003070.5(SMARCA2):​c.31C>A​(p.Pro11Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P11S) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SMARCA2 NM_003070.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.16

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]

ACMG classification

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=0.26915467).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMARCA2	NM_003070.5	c.31C>A	p.Pro11Thr	missense_variant	2/34	ENST00000349721.8
SMARCA2	NM_001289396.1	c.31C>A	p.Pro11Thr	missense_variant	2/34
SMARCA2	NM_139045.4	c.31C>A	p.Pro11Thr	missense_variant	2/33
SMARCA2	NM_001289397.2	c.31C>A	p.Pro11Thr	missense_variant	2/33

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMARCA2	ENST00000349721.8	c.31C>A	p.Pro11Thr	missense_variant	2/34	5	NM_003070.5	P2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Nicolaides-Baraitser syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Genomic Research Center, Shahid Beheshti University of Medical Sciences

Dec 18, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Uncertain	0.11	D
BayesDel_noAF	Uncertain	-0.080
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.081	.;.;T;T;T;T;T;.;T;T;T
Eigen	Benign	0.17
Eigen_PC	Uncertain	0.31
FATHMM_MKL	Uncertain	0.87	D
LIST_S2	Uncertain	0.96	.;D;.;.;.;D;D;D;D;D;D
M_CAP	Benign	0.036	D
MetaRNN	Benign	0.27	T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Uncertain	0.19	D
MutationAssessor	Benign	1.7	L;.;.;L;.;.;.;L;.;.;L
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Uncertain	0.77	T
PROVEAN	Benign	-1.9	N;D;.;N;.;.;D;N;D;.;N
REVEL	Uncertain	0.33
Sift	Uncertain	0.014	D;D;.;D;.;.;D;D;D;.;D
Sift4G	Uncertain	0.033	D;D;.;D;.;.;D;D;D;.;D
Polyphen		0.42	B;.;.;B;.;.;.;B;.;.;B
Vest4		0.44
MutPred		0.16		Gain of phosphorylation at P11 (P = 0.0194);Gain of phosphorylation at P11 (P = 0.0194);Gain of phosphorylation at P11 (P = 0.0194);Gain of phosphorylation at P11 (P = 0.0194);Gain of phosphorylation at P11 (P = 0.0194);Gain of phosphorylation at P11 (P = 0.0194);Gain of phosphorylation at P11 (P = 0.0194);Gain of phosphorylation at P11 (P = 0.0194);Gain of phosphorylation at P11 (P = 0.0194);Gain of phosphorylation at P11 (P = 0.0194);Gain of phosphorylation at P11 (P = 0.0194);
MVP		0.55
MPC		0.051
ClinPred		0.84	D
GERP RS		5.5
Varity_R		0.20
gMVP		0.26

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

Other links and lift over

dbSNP: rs145516397; hg19: chr9-2029053;