rs1555781082

Variant names:

• chr19-11026328-C-A
• rs1555781082
• NM_001387283.1:c.3197C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-11026328-C-A
• chr19-11026328-C-G
• chr19-11026328-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2 PP2 BP4_Moderate

The NM_003072.5(SMARCA4):​c.3197C>A​(p.Thr1066Asn) variant causes a missense change involving the alteration of a 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 (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SMARCA4 NM_003072.5 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:2
• Conservation: PhyloP100: 7.43

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the SMARCA4 gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 59 curated pathogenic missense variants (we use a threshold of 10). The gene has 56 curated benign missense variants. Gene score misZ: 6.8459 (above the threshold of 3.09). Trascript score misZ: 8.7957 (above the threshold of 3.09). GenCC associations: The gene is linked to uterine corpus sarcoma, Coffin-Siris syndrome 1, intellectual disability, autosomal dominant 16, rhabdoid tumor predisposition syndrome 2, familial rhabdoid tumor, hereditary nonpolyposis colon cancer, Coffin-Siris syndrome.
• BP4: Computational evidence support a benign effect (MetaRNN=0.22991744).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.3197C>A	p.Thr1066Asn	missense_variant	Exon 23 of 36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.3197C>A	p.Thr1066Asn	missense_variant	Exon 23 of 35	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.3197C>A	p.Thr1066Asn	missense_variant	Exon 23 of 36		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.3197C>A	p.Thr1066Asn	missense_variant	Exon 23 of 35	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.3197C>A	p.Thr1066Asn	missense_variant	Exon 23 of 35			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.3197C>A	p.Thr1066Asn	missense_variant	Exon 24 of 35	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.3197C>A	p.Thr1066Asn	missense_variant	Exon 23 of 34			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.3197C>A	p.Thr1066Asn	missense_variant	Exon 23 of 34			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.3197C>A	p.Thr1066Asn	missense_variant	Exon 24 of 35	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.2609C>A	p.Thr870Asn	missense_variant	Exon 20 of 32			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.1841C>A	p.Thr614Asn	missense_variant	Exon 16 of 28			ENSP00000495599.1
SMARCA4	ENST00000644065.1	c.1922C>A	p.Thr641Asn	missense_variant	Exon 16 of 27			ENSP00000493615.1
SMARCA4	ENST00000642350.1	c.1682C>A	p.Thr561Asn	missense_variant	Exon 15 of 27			ENSP00000495355.1
SMARCA4	ENST00000643857.1	c.1550C>A	p.Thr517Asn	missense_variant	Exon 14 of 25			ENSP00000494159.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

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

Sep 10, 2020

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with SMARCA4-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces threonine with asparagine at codon 1066 of the SMARCA4 protein (p.Thr1066Asn). The threonine residue is moderately conserved and there is a small physicochemical difference between threonine and asparagine. -

Hereditary cancer-predisposing syndrome Uncertain:1

Dec 28, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.T1066N variant (also known as c.3197C>A), located in coding exon 22 of the SMARCA4 gene, results from a C to A substitution at nucleotide position 3197. The threonine at codon 1066 is replaced by asparagine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. 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	0.19
BayesDel_addAF	Benign	-0.048	T
BayesDel_noAF	Benign	-0.31
CADD	Uncertain	24
DANN	Benign	0.91
DEOGEN2	Benign	0.21	T;.;T;.;.;.;.;.;.;.;T;.;.;.;.;.;T;T;.;.;.;.
Eigen	Benign	-0.16
Eigen_PC	Benign	-0.0012
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.93	.;D;.;.;.;.;D;.;.;.;D;.;D;D;D;D;D;D;D;D;D;D
M_CAP	Uncertain	0.11	D
MetaRNN	Benign	0.23	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.71	T
MutationAssessor	Benign	0.76	N;.;.;.;N;N;.;N;N;N;N;N;N;N;N;N;.;.;.;.;.;.
PrimateAI	Uncertain	0.77	T
PROVEAN	Benign	-0.49	N;.;.;.;.;.;.;.;.;.;N;.;N;.;N;.;D;N;.;.;.;.
REVEL	Benign	0.15
Sift	Benign	0.60	T;.;.;.;.;.;.;.;.;.;T;.;T;.;T;.;D;T;.;.;.;.
Sift4G	Benign	0.31	T;.;.;.;.;.;.;.;.;.;T;.;T;T;T;T;T;T;.;.;.;.
Polyphen		0.0010	B;.;B;.;.;.;.;.;.;.;B;.;.;.;.;.;.;B;.;.;.;.
Vest4		0.29
MutPred		0.39		Gain of catalytic residue at T1066 (P = 0.1075);Gain of catalytic residue at T1066 (P = 0.1075);Gain of catalytic residue at T1066 (P = 0.1075);Gain of catalytic residue at T1066 (P = 0.1075);Gain of catalytic residue at T1066 (P = 0.1075);Gain of catalytic residue at T1066 (P = 0.1075);Gain of catalytic residue at T1066 (P = 0.1075);Gain of catalytic residue at T1066 (P = 0.1075);Gain of catalytic residue at T1066 (P = 0.1075);Gain of catalytic residue at T1066 (P = 0.1075);Gain of catalytic residue at T1066 (P = 0.1075);Gain of catalytic residue at T1066 (P = 0.1075);Gain of catalytic residue at T1066 (P = 0.1075);Gain of catalytic residue at T1066 (P = 0.1075);Gain of catalytic residue at T1066 (P = 0.1075);Gain of catalytic residue at T1066 (P = 0.1075);.;Gain of catalytic residue at T1066 (P = 0.1075);.;.;.;.;
MVP		0.65
MPC		1.7
ClinPred		0.50	D
GERP RS		4.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.8
Varity_R		0.062
gMVP		0.91

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: rs1555781082; hg19: chr19-11137004;