chr19-10991262-C-T

Position:

• chr19-10991262-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2 PP2 PP3 BP6

The NM_003072.5(SMARCA4):​c.1358C>T​(p.Thr453Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: SMARCA4 NM_003072.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:2 B:1
• Conservation: PhyloP100: 7.88

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 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.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.752
• BP6: Variant 19-10991262-C-T is Benign according to our data. Variant chr19-10991262-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 374051.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=2}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.1358C>T	p.Thr453Ile	missense_variant	8/36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.1358C>T	p.Thr453Ile	missense_variant	8/35	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.1358C>T	p.Thr453Ile	missense_variant	8/36		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.1358C>T	p.Thr453Ile	missense_variant	8/35	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.1358C>T	p.Thr453Ile	missense_variant	8/35			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.1358C>T	p.Thr453Ile	missense_variant	9/35	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.1358C>T	p.Thr453Ile	missense_variant	8/34			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.1358C>T	p.Thr453Ile	missense_variant	8/34			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.1358C>T	p.Thr453Ile	missense_variant	9/35	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.770C>T	p.Thr257Ile	missense_variant	5/32			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.2C>T	p.Thr1Ile	missense_variant	1/28			ENSP00000495599.1
SMARCA4	ENST00000644065.1	c.86C>T	p.Thr29Ile	missense_variant	1/27			ENSP00000493615.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

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

Uncertain significance, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Rhabdoid tumor predisposition syndrome 2 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Oct 27, 2019

This variant was classified as: Uncertain significance. The available evidence on this variant's pathogenicity is insufficient or conflicting. The following ACMG criteria were applied in classifying this variant: PM2,PP3,BS2. -

Ventricular septal defect;C0038379:Strabismus;C0424731:Single transverse palmar crease;C0557874:Global developmental delay;C1306710:Facial asymmetry Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Jan 23, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.19	D
BayesDel_noAF	Uncertain	0.030
CADD	Pathogenic	27
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.83	D;.;T;.;.;.;.;.;.;.;D;.;.;.;.;.;T;T
Eigen	Pathogenic	0.87
Eigen_PC	Pathogenic	0.81
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.99	.;D;.;.;.;.;D;.;.;.;D;.;D;D;D;D;D;D
M_CAP	Pathogenic	0.30	D
MetaRNN	Pathogenic	0.75	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	-0.26	T
MutationAssessor	Pathogenic	3.4	M;.;.;.;M;M;.;M;M;M;M;M;M;M;M;M;.;.
PrimateAI	Pathogenic	0.92	D
PROVEAN	Pathogenic	-5.6	D;.;.;.;.;.;.;.;.;.;D;.;D;.;D;.;D;D
REVEL	Uncertain	0.49
Sift	Uncertain	0.0010	D;.;.;.;.;.;.;.;.;.;D;.;D;.;D;.;D;D
Sift4G	Uncertain	0.031	D;.;.;.;.;.;.;.;.;.;D;.;D;D;D;D;D;D
Polyphen		1.0	D;.;D;.;.;.;.;.;.;.;D;.;.;.;.;.;.;D
Vest4		0.73
MutPred		0.41		Loss of phosphorylation at T453 (P = 0.0238);Loss of phosphorylation at T453 (P = 0.0238);Loss of phosphorylation at T453 (P = 0.0238);Loss of phosphorylation at T453 (P = 0.0238);Loss of phosphorylation at T453 (P = 0.0238);Loss of phosphorylation at T453 (P = 0.0238);Loss of phosphorylation at T453 (P = 0.0238);Loss of phosphorylation at T453 (P = 0.0238);Loss of phosphorylation at T453 (P = 0.0238);Loss of phosphorylation at T453 (P = 0.0238);Loss of phosphorylation at T453 (P = 0.0238);Loss of phosphorylation at T453 (P = 0.0238);Loss of phosphorylation at T453 (P = 0.0238);Loss of phosphorylation at T453 (P = 0.0238);Loss of phosphorylation at T453 (P = 0.0238);Loss of phosphorylation at T453 (P = 0.0238);Loss of phosphorylation at T453 (P = 0.0238);Loss of phosphorylation at T453 (P = 0.0238);
MVP		0.66
MPC		2.6
ClinPred		0.87	D
GERP RS		4.9
Varity_R		0.78
gMVP		0.99

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: rs1057518862; hg19: chr19-11101938;