19-10987672-T-G

Position:

• chr19-10987672-T-G

Variant summary

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

The NM_003072.5(SMARCA4):​c.866T>G​(p.Met289Arg) 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 (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SMARCA4 NM_003072.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.23

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 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), 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=0.28281552).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.866T>G	p.Met289Arg	missense_variant	6/36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.866T>G	p.Met289Arg	missense_variant	6/35	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.866T>G	p.Met289Arg	missense_variant	6/36		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.866T>G	p.Met289Arg	missense_variant	6/35	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.866T>G	p.Met289Arg	missense_variant	6/35			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.866T>G	p.Met289Arg	missense_variant	7/35	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.866T>G	p.Met289Arg	missense_variant	6/34			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.866T>G	p.Met289Arg	missense_variant	6/34			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.866T>G	p.Met289Arg	missense_variant	7/35	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.278T>G	p.Met93Arg	missense_variant	3/32			ENSP00000496004.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Rhabdoid tumor predisposition syndrome 2 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 09, 2023

This sequence change replaces methionine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 289 of the SMARCA4 protein (p.Met289Arg). 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. 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 SMARCA4 protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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	Uncertain	0.45
BayesDel_addAF	Pathogenic	0.29	D
BayesDel_noAF	Pathogenic	0.18
CADD	Uncertain	25
DANN	Benign	0.51
DEOGEN2	Benign	0.39	T;.;T;.;.;.;.;.;.;.;T;.;.;.;.;.;T;T
Eigen	Benign	-0.36
Eigen_PC	Benign	-0.34
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Uncertain	0.88	.;D;.;.;.;.;D;.;.;.;D;.;D;D;D;D;D;D
M_CAP	Uncertain	0.27	D
MetaRNN	Benign	0.28	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.50	T
MutationAssessor	Benign	1.4	L;.;.;.;L;L;.;L;L;L;L;L;L;L;L;L;.;.
PrimateAI	Uncertain	0.66	T
PROVEAN	Benign	-1.5	N;.;.;.;.;.;.;.;.;.;N;.;N;.;N;.;N;N
REVEL	Uncertain	0.58
Sift	Benign	0.28	T;.;.;.;.;.;.;.;.;.;T;.;T;.;T;.;T;T
Sift4G	Benign	0.58	T;.;.;.;.;.;.;.;.;.;T;.;T;T;T;T;T;T
Polyphen		0.85	P;.;P;.;.;.;.;.;.;.;P;.;.;.;.;.;.;P
Vest4		0.72
MutPred		0.28		Gain of methylation at M289 (P = 0.0446);Gain of methylation at M289 (P = 0.0446);Gain of methylation at M289 (P = 0.0446);Gain of methylation at M289 (P = 0.0446);Gain of methylation at M289 (P = 0.0446);Gain of methylation at M289 (P = 0.0446);Gain of methylation at M289 (P = 0.0446);Gain of methylation at M289 (P = 0.0446);Gain of methylation at M289 (P = 0.0446);Gain of methylation at M289 (P = 0.0446);Gain of methylation at M289 (P = 0.0446);Gain of methylation at M289 (P = 0.0446);Gain of methylation at M289 (P = 0.0446);Gain of methylation at M289 (P = 0.0446);Gain of methylation at M289 (P = 0.0446);Gain of methylation at M289 (P = 0.0446);Gain of methylation at M289 (P = 0.0446);Gain of methylation at M289 (P = 0.0446);
MVP		0.97
MPC		0.41
ClinPred		0.62	D
GERP RS		3.3
Varity_R		0.47
gMVP		0.15

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: chr19-11098348;