chr19-11027926-G-T

Variant names:

• chr19-11027926-G-T
• rs373590049
• NM_001387283.1:c.3358G>T

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2 PP3

The NM_001387283.1(SMARCA4):​c.3358G>T​(p.Gly1120Cys) 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 pathogenic 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. G1120S) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SMARCA4 NM_001387283.1 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:2
• Conservation: PhyloP100: 2.43
• Publications: 0 publications found

Genes affected

SMARCA4 (HGNC:11100): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4) The protein encoded by this gene is a member of the SWI/SNF family of proteins and is 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. In addition, this protein can bind BRCA1, as well as regulate the expression of the tumorigenic protein CD44. Mutations in this gene cause rhabdoid tumor predisposition syndrome type 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]

SMARCA4 Gene-Disease associations (from GenCC):

• Coffin-Siris syndrome

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet, Illumina
• intellectual disability, autosomal dominant 16

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
• rhabdoid tumor predisposition syndrome 2

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, ClinGen, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), G2P
• uterine corpus sarcoma

  Inheritance: AR Classification: MODERATE Submitted by: Genomics England PanelApp
• familial rhabdoid tumor

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary nonpolyposis colon cancer

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Uncertain_significance. The variant received 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.836

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.3358G>T	p.Gly1120Cys	missense_variant	Exon 24 of 36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.3358G>T	p.Gly1120Cys	missense_variant	Exon 24 of 35	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.3358G>T	p.Gly1120Cys	missense_variant	Exon 24 of 36		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.3358G>T	p.Gly1120Cys	missense_variant	Exon 24 of 35	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.3358G>T	p.Gly1120Cys	missense_variant	Exon 24 of 35			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.3358G>T	p.Gly1120Cys	missense_variant	Exon 25 of 35	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.3358G>T	p.Gly1120Cys	missense_variant	Exon 24 of 34			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.3358G>T	p.Gly1120Cys	missense_variant	Exon 24 of 34			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.3358G>T	p.Gly1120Cys	missense_variant	Exon 25 of 35	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.2770G>T	p.Gly924Cys	missense_variant	Exon 21 of 32			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.2002G>T	p.Gly668Cys	missense_variant	Exon 17 of 28			ENSP00000495599.1
SMARCA4	ENST00000644065.1	c.2083G>T	p.Gly695Cys	missense_variant	Exon 17 of 27			ENSP00000493615.1
SMARCA4	ENST00000642350.1	c.1843G>T	p.Gly615Cys	missense_variant	Exon 16 of 27			ENSP00000495355.1
SMARCA4	ENST00000643857.1	c.1711G>T	p.Gly571Cys	missense_variant	Exon 15 of 25			ENSP00000494159.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Rhabdoid tumor predisposition syndrome 2 Uncertain:1

Apr 29, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces glycine, which is neutral and non-polar, with cysteine, which is neutral and slightly polar, at codon 1120 of the SMARCA4 protein (p.Gly1120Cys). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SMARCA4-related conditions. ClinVar contains an entry for this variant (Variation ID: 1481674). 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 expected to disrupt SMARCA4 protein function with a positive predictive value of 95%. 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. -

Hereditary cancer-predisposing syndrome Uncertain:1

Jan 21, 2025

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.G1120C variant (also known as c.3358G>T), located in coding exon 23 of the SMARCA4 gene, results from a G to T substitution at nucleotide position 3358. The glycine at codon 1120 is replaced by cysteine, an amino acid with highly dissimilar properties. This amino acid position is not well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on the available evidence, the clinical significance of this variant remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.25
BayesDel_addAF	Uncertain	0.13	D
BayesDel_noAF	Uncertain	-0.050
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.93	D;.;D;.;.;.;.;.;.;.;D;.;.;.;.;.;T;D;.;.;.
Eigen	Pathogenic	0.80
Eigen_PC	Pathogenic	0.70
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.95	.;D;.;.;.;.;D;.;.;.;D;.;D;D;D;D;D;D;D;D;D
M_CAP	Pathogenic	0.57	D
MetaRNN	Pathogenic	0.84	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	0.82	D
MutationAssessor	Pathogenic	3.4	M;.;.;.;M;M;.;M;M;M;M;M;M;M;M;M;.;.;.;.;.
PhyloP100		2.4
PrimateAI	Pathogenic	0.83	D
PROVEAN	Pathogenic	-5.1	D;.;.;.;.;.;.;.;.;.;D;.;D;.;D;.;.;D;.;.;.
REVEL	Uncertain	0.63
Sift	Uncertain	0.0010	D;.;.;.;.;.;.;.;.;.;D;.;D;.;D;.;.;D;.;.;.
Sift4G	Uncertain	0.0030	D;.;.;.;.;.;.;.;.;.;D;.;D;D;D;D;D;D;.;.;.
Polyphen		0.99	D;.;D;.;.;.;.;.;.;.;D;.;.;.;.;.;.;D;.;.;.
Vest4		0.58
MutPred		0.67		Gain of ubiquitination at K1122 (P = 0.0624);Gain of ubiquitination at K1122 (P = 0.0624);Gain of ubiquitination at K1122 (P = 0.0624);Gain of ubiquitination at K1122 (P = 0.0624);Gain of ubiquitination at K1122 (P = 0.0624);Gain of ubiquitination at K1122 (P = 0.0624);Gain of ubiquitination at K1122 (P = 0.0624);Gain of ubiquitination at K1122 (P = 0.0624);Gain of ubiquitination at K1122 (P = 0.0624);Gain of ubiquitination at K1122 (P = 0.0624);Gain of ubiquitination at K1122 (P = 0.0624);Gain of ubiquitination at K1122 (P = 0.0624);Gain of ubiquitination at K1122 (P = 0.0624);Gain of ubiquitination at K1122 (P = 0.0624);Gain of ubiquitination at K1122 (P = 0.0624);Gain of ubiquitination at K1122 (P = 0.0624);.;Gain of ubiquitination at K1122 (P = 0.0624);.;.;.;
MVP		0.87
MPC		2.7
ClinPred		0.97	D
GERP RS		5.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.90
gMVP		0.98
Mutation Taster		=75/25	polymorphism

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

Other links and lift over

dbSNP: rs373590049; hg19: chr19-11138602;