NM_001387283.1:c.3868C>G

Variant names:

• chr19-11033860-C-G
• rs1555784851
• NM_001387283.1:c.3868C>G

Variant summary

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

The NM_001387283.1(SMARCA4):​c.3868C>G​(p.Leu1290Val) 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. 13/21 in silico tools predict 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. L1290P) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SMARCA4 NM_001387283.1 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:3
• Conservation: PhyloP100: 1.95

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]

ENSG00000278643 (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 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=0.21047932).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.3868C>G	p.Leu1290Val	missense_variant	Exon 27 of 36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.3868C>G	p.Leu1290Val	missense_variant	Exon 27 of 35	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.3868C>G	p.Leu1290Val	missense_variant	Exon 27 of 36		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.3868C>G	p.Leu1290Val	missense_variant	Exon 27 of 35	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643995.1	c.3280C>G	p.Leu1094Val	missense_variant	Exon 24 of 32			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.2512C>G	p.Leu838Val	missense_variant	Exon 20 of 28			ENSP00000495599.1
SMARCA4	ENST00000642350.1	c.2353C>G	p.Leu785Val	missense_variant	Exon 19 of 27			ENSP00000495355.1
SMARCA4	ENST00000643857.1	c.2221C>G	p.Leu741Val	missense_variant	Exon 18 of 25			ENSP00000494159.1
SMARCA4	ENST00000643549.1	c.3775-263C>G		intron_variant	Intron 26 of 34			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.3775-263C>G		intron_variant	Intron 27 of 34	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.3775-263C>G		intron_variant	Intron 26 of 33			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.3775-263C>G		intron_variant	Intron 26 of 33			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.3775-263C>G		intron_variant	Intron 27 of 34	5		ENSP00000464778.1
SMARCA4	ENST00000644065.1	c.2500-263C>G		intron_variant	Intron 19 of 26			ENSP00000493615.1
SMARCA4	ENST00000538456.4	c.31-263C>G		intron_variant	Intron 1 of 7	3		ENSP00000495197.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Intellectual disability, autosomal dominant 16 Uncertain:1

Jul 15, 2021

Genome-Nilou Lab

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Rhabdoid tumor predisposition syndrome 2 Uncertain:1

Jan 22, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces leucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1290 of the SMARCA4 protein (p.Leu1290Val). 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: 470370). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SMARCA4 protein function. 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

Nov 26, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.L1290V variant (also known as c.3868C>G), located in coding exon 26 of the SMARCA4 gene, results from a C to G substitution at nucleotide position 3868. The leucine at codon 1290 is replaced by valine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. This variant was detected in multiple individuals with no reported features of Coffin-Siris syndrome (Ambry internal data). Based on the supporting evidence, the association of this alteration with rhabdoid tumor predisposition syndrome is unknown; however, the association of this alteration with Coffin-Siris syndrome is unlikely. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.066
BayesDel_addAF	Uncertain	0.012	T
BayesDel_noAF	Benign	-0.22
CADD	Uncertain	24
DANN	Benign	0.94
DEOGEN2	Benign	0.20	T;T;T;T;.;.
Eigen	Benign	0.18
Eigen_PC	Uncertain	0.29
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Benign	0.76	.;.;T;T;T;T
M_CAP	Benign	0.039	D
MetaRNN	Benign	0.21	T;T;T;T;T;T
MetaSVM	Uncertain	0.14	D
MutationAssessor	Benign	0.63	N;.;N;.;.;.
PrimateAI	Uncertain	0.78	T
PROVEAN	Benign	-0.23	N;.;N;.;.;.
REVEL	Benign	0.28
Sift	Benign	0.21	T;.;T;.;.;.
Sift4G	Benign	0.91	T;.;T;T;.;.
Polyphen		0.46	P;P;P;P;.;.
Vest4		0.24
MutPred		0.32		Gain of methylation at K1291 (P = 0.0335);Gain of methylation at K1291 (P = 0.0335);Gain of methylation at K1291 (P = 0.0335);Gain of methylation at K1291 (P = 0.0335);.;.;
MVP		0.76
MPC		1.5
ClinPred		0.38	T
GERP RS		5.2
Varity_R		0.12
gMVP		0.52

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: rs1555784851; hg19: chr19-11144536;