chr19-11041336-C-A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4BP6_ModerateBP7

The NM_001387283.1(SMARCA4):c.4296C>A(p.Ile1432Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,632 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. I1432I) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

SMARCA4
NM_001387283.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

Publications

0 publications found

Variant links:

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

SMARCA4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.14).

BP6

Variant 19-11041336-C-A is Benign according to our data. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-11041336-C-A is described in CliVar as Likely_benign. Clinvar id is 4084758.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.48 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCA4	NM_001387283.1 link	c.4296C>A	p.Ile1432Ile	synonymous_variant	Exon 31 of 36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5 link	c.4200C>A	p.Ile1400Ile	synonymous_variant	Exon 30 of 35	ENST00000344626.10	NP_003063.2	P51532-1A7E2E1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SMARCA4	ENST00000646693.2 link	c.4296C>A	p.Ile1432Ile	synonymous_variant	Exon 31 of 36		NM_001387283.1	ENSP00000495368.1	Q9HBD4
SMARCA4	ENST00000344626.10 link	c.4200C>A	p.Ile1400Ile	synonymous_variant	Exon 30 of 35	1	NM_003072.5	ENSP00000343896.4	P51532-1
SMARCA4	ENST00000643549.1 link	c.4206C>A	p.Ile1402Ile	synonymous_variant	Exon 30 of 35			ENSP00000493975.1	A0A2R8Y4P4
SMARCA4	ENST00000541122.6 link	c.4110C>A	p.Ile1370Ile	synonymous_variant	Exon 30 of 35	5		ENSP00000445036.2	P51532-4
SMARCA4	ENST00000643296.1 link	c.4110C>A	p.Ile1370Ile	synonymous_variant	Exon 29 of 34			ENSP00000496635.1	P51532-4
SMARCA4	ENST00000644737.1 link	c.4110C>A	p.Ile1370Ile	synonymous_variant	Exon 29 of 34			ENSP00000495548.1	P51532-4
SMARCA4	ENST00000589677.5 link	c.4110C>A	p.Ile1370Ile	synonymous_variant	Exon 30 of 35	5		ENSP00000464778.1	P51532-3
SMARCA4	ENST00000643995.1 link	c.3621C>A	p.Ile1207Ile	synonymous_variant	Exon 27 of 32			ENSP00000496004.1	A0A2R8YGG3
SMARCA4	ENST00000644963.1 link	c.2853C>A	p.Ile951Ile	synonymous_variant	Exon 23 of 28			ENSP00000495599.1	A0A2R8YG32
SMARCA4	ENST00000644065.1 link	c.2835C>A	p.Ile945Ile	synonymous_variant	Exon 22 of 27			ENSP00000493615.1	A0A2R8Y440
SMARCA4	ENST00000642350.1 link	c.2694C>A	p.Ile898Ile	synonymous_variant	Exon 22 of 27			ENSP00000495355.1	A0A2R8Y6N0
SMARCA4	ENST00000643857.1 link	c.2562C>A	p.Ile854Ile	synonymous_variant	Exon 21 of 25			ENSP00000494159.1	A0A2R8Y526
SMARCA4	ENST00000538456.4 link	c.366C>A	p.Ile122Ile	synonymous_variant	Exon 4 of 8	3		ENSP00000495197.1	A0A2R8YFK5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.85e-7

AC:

AN:

1459632

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

726160

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33478

American (AMR)

AF:

0.00

AC:

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26132

East Asian (EAS)

AF:

0.00

AC:

AN:

39694

South Asian (SAS)

AF:

0.00

AC:

AN:

86248

European-Finnish (FIN)

AF:

0.00

AC:

AN:

51274

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5754

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1111944

Other (OTH)

AF:

0.0000166

AC:

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.14

CADD

Benign

9.2

(source)

DANN

Benign

0.78

PhyloP100

-1.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=98/2

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over