rs878854217

Positions:

• chr19-11034928-C-G
• chr19-11034928-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.3966C>G​(p.Asp1322Glu) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SMARCA4 NM_003072.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.50

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 (HGNC:):

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 gene, where missense usually causes diseases (based on misZ statistic), SMARCA4. . Gene score misZ 6.8459 (greater than the threshold 3.09). Trascript score misZ 8.7957 (greater than threshold 3.09). GenCC has associacion of gene with 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=0.16327906).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.3966C>G	p.Asp1322Glu	missense_variant	29/36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.3966C>G	p.Asp1322Glu	missense_variant	29/35	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.3966C>G	p.Asp1322Glu	missense_variant	29/36		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.3966C>G	p.Asp1322Glu	missense_variant	29/35	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.3867C>G	p.Asp1289Glu	missense_variant	28/35			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.3867C>G	p.Asp1289Glu	missense_variant	29/35	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.3867C>G	p.Asp1289Glu	missense_variant	28/34			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.3867C>G	p.Asp1289Glu	missense_variant	28/34			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.3867C>G	p.Asp1289Glu	missense_variant	29/35	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.3378C>G	p.Asp1126Glu	missense_variant	26/32			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.2610C>G	p.Asp870Glu	missense_variant	22/28			ENSP00000495599.1
SMARCA4	ENST00000644065.1	c.2592C>G	p.Asp864Glu	missense_variant	21/27			ENSP00000493615.1
SMARCA4	ENST00000642350.1	c.2451C>G	p.Asp817Glu	missense_variant	21/27			ENSP00000495355.1
SMARCA4	ENST00000643857.1	c.2319C>G	p.Asp773Glu	missense_variant	20/25			ENSP00000494159.1
SMARCA4	ENST00000538456.4	c.123C>G	p.Asp41Glu	missense_variant	3/8	3		ENSP00000495197.1

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

Hereditary cancer-predisposing syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 06, 2024

The p.D1322E variant (also known as c.3966C>G), located in coding exon 28 of the SMARCA4 gene, results from a C to G substitution at nucleotide position 3966. The aspartic acid at codon 1322 is replaced by glutamic acid, an amino acid with highly similar properties. This amino acid position is conserved. 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	Pathogenic	0.64
BayesDel_addAF	Uncertain	0.088	D
BayesDel_noAF	Benign	-0.11
CADD	Benign	22
DANN	Benign	0.61
DEOGEN2	Benign	0.21	T;.;T;.;.;.;.;.;.;.;T;.;.;.;.;.;T;T;.;.;.;.
Eigen	Benign	0.021
Eigen_PC	Benign	0.16
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Uncertain	0.93	.;D;.;.;.;.;D;.;.;.;D;.;D;D;D;D;D;D;D;D;D;D
M_CAP	Uncertain	0.17	D
MetaRNN	Benign	0.16	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	-0.30	N;.;.;.;.;.;.;.;.;.;N;.;.;.;.;.;.;.;.;.;.;.
PrimateAI	Pathogenic	0.84	D
PROVEAN	Benign	-0.18	N;.;.;.;.;.;.;.;.;.;N;.;N;.;N;.;.;.;.;.;.;.
REVEL	Uncertain	0.37
Sift	Benign	1.0	T;.;.;.;.;.;.;.;.;.;T;.;T;.;T;.;.;.;.;.;.;.
Sift4G	Benign	1.0	T;.;.;.;.;.;.;.;.;.;T;.;T;T;T;T;T;T;.;.;.;.
Polyphen		0.032	B;.;B;.;.;.;.;.;.;.;B;.;.;.;.;.;.;B;.;.;.;.
Vest4		0.52
MutPred		0.21		Gain of helix (P = 0.0199);.;Gain of helix (P = 0.0199);.;.;.;.;.;.;.;Gain of helix (P = 0.0199);.;.;.;.;.;.;Gain of helix (P = 0.0199);.;.;.;.;
MVP		0.82
MPC		2.0
ClinPred		0.72	D
GERP RS		3.9
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.7
Varity_R		0.060
gMVP		0.82

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-11145604;