chr19-11007948-C-G

Variant names:

• chr19-11007948-C-G
• rs878854203
• NM_001387283.1:c.2048C>G

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP6

The NM_001387283.1(SMARCA4):​c.2048C>G​(p.Pro683Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,498 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P683L) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: SMARCA4 NM_001387283.1 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:2 B:1
• Conservation: PhyloP100: 2.74
• 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: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2265366).
• BP6: Variant 19-11007948-C-G is Benign according to our data. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387. Variant chr19-11007948-C-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 238387.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.2048C>G	p.Pro683Arg	missense_variant	Exon 14 of 36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.2048C>G	p.Pro683Arg	missense_variant	Exon 14 of 35	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.2048C>G	p.Pro683Arg	missense_variant	Exon 14 of 36		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.2048C>G	p.Pro683Arg	missense_variant	Exon 14 of 35	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.2048C>G	p.Pro683Arg	missense_variant	Exon 14 of 35			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.2048C>G	p.Pro683Arg	missense_variant	Exon 15 of 35	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.2048C>G	p.Pro683Arg	missense_variant	Exon 14 of 34			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.2048C>G	p.Pro683Arg	missense_variant	Exon 14 of 34			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.2048C>G	p.Pro683Arg	missense_variant	Exon 15 of 35	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.1460C>G	p.Pro487Arg	missense_variant	Exon 11 of 32			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.692C>G	p.Pro231Arg	missense_variant	Exon 7 of 28			ENSP00000495599.1
SMARCA4	ENST00000644065.1	c.773C>G	p.Pro258Arg	missense_variant	Exon 7 of 27			ENSP00000493615.1
SMARCA4	ENST00000642350.1	c.533C>G	p.Pro178Arg	missense_variant	Exon 6 of 27			ENSP00000495355.1
SMARCA4	ENST00000643857.1	c.401C>G	p.Pro134Arg	missense_variant	Exon 5 of 25			ENSP00000494159.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461498 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 727076

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 33462

American (AMR) AF: 0.00 AC: 0 AN: 44716

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26126

East Asian (EAS) AF: 0.00 AC: 0 AN: 39690

South Asian (SAS) AF: 0.00 AC: 0 AN: 86242

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53360

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 8.99e-7 AC: 1 AN: 1111758

Other (OTH) AF: 0.00 AC: 0 AN: 60376

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 31

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:2 Benign:1

Revision: criteria provided, conflicting classifications

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

Aug 19, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 683 of the SMARCA4 protein (p.Pro683Arg). 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: 238387). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt SMARCA4 protein function with a negative 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 Benign:1

Aug 20, 2021

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Uncertain	0.041	T
BayesDel_noAF	Benign	-0.18
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Benign	0.34	T;.;T;.;.;.;.;.;.;.;T;.;.;.;.;.;T;T;.;.;.
Eigen	Benign	-0.046
Eigen_PC	Benign	0.18
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.95	.;D;.;.;.;.;D;.;.;.;D;.;D;D;D;D;D;D;D;D;D
M_CAP	Benign	0.045	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
MetaSVM	Benign	-0.58	T
MutationAssessor	Benign	0.90	L;.;.;.;L;L;.;L;L;L;L;L;L;L;L;L;.;.;.;.;.
PhyloP100		2.7
PrimateAI	Uncertain	0.69	T
PROVEAN	Benign	-1.1	N;.;.;.;.;.;.;.;.;.;N;.;N;.;N;.;.;N;.;.;.
REVEL	Uncertain	0.31
Sift	Benign	0.061	T;.;.;.;.;.;.;.;.;.;T;.;T;.;T;.;.;T;.;.;.
Sift4G	Benign	0.24	T;.;.;.;.;.;.;.;.;.;T;.;T;T;T;T;T;T;.;.;.
Polyphen		0.039	B;.;B;.;.;.;.;.;.;.;B;.;.;.;.;.;.;B;.;.;.
Vest4		0.64
MutPred		0.22		Loss of glycosylation at P683 (P = 0.0392);Loss of glycosylation at P683 (P = 0.0392);Loss of glycosylation at P683 (P = 0.0392);Loss of glycosylation at P683 (P = 0.0392);Loss of glycosylation at P683 (P = 0.0392);Loss of glycosylation at P683 (P = 0.0392);Loss of glycosylation at P683 (P = 0.0392);Loss of glycosylation at P683 (P = 0.0392);Loss of glycosylation at P683 (P = 0.0392);Loss of glycosylation at P683 (P = 0.0392);Loss of glycosylation at P683 (P = 0.0392);Loss of glycosylation at P683 (P = 0.0392);Loss of glycosylation at P683 (P = 0.0392);Loss of glycosylation at P683 (P = 0.0392);Loss of glycosylation at P683 (P = 0.0392);Loss of glycosylation at P683 (P = 0.0392);.;Loss of glycosylation at P683 (P = 0.0392);.;.;.;
MVP		0.56
MPC		1.4
ClinPred		0.45	T
GERP RS		5.6
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.1
Varity_R		0.094
gMVP		0.83
Mutation Taster		=81/19	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: rs878854203; hg19: chr19-11118624;