19-10991290-C-G

Position:

• chr19-10991290-C-G

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2 PP2 BP4_Strong

The NM_003072.5(SMARCA4):​c.1386C>G​(p.Ile462Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,456,698 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: SMARCA4 NM_003072.5 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:3
• Conservation: PhyloP100: -4.51

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 Likely_benign. Variant got -1 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=0.040569186).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.1386C>G	p.Ile462Met	missense_variant	8/36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.1386C>G	p.Ile462Met	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.1386C>G	p.Ile462Met	missense_variant	8/36		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.1386C>G	p.Ile462Met	missense_variant	8/35	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.1386C>G	p.Ile462Met	missense_variant	8/35			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.1386C>G	p.Ile462Met	missense_variant	9/35	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.1386C>G	p.Ile462Met	missense_variant	8/34			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.1386C>G	p.Ile462Met	missense_variant	8/34			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.1386C>G	p.Ile462Met	missense_variant	9/35	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.798C>G	p.Ile266Met	missense_variant	5/32			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.30C>G	p.Ile10Met	missense_variant	1/28			ENSP00000495599.1
SMARCA4	ENST00000644065.1	c.114C>G	p.Ile38Met	missense_variant	1/27			ENSP00000493615.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000206 AC: 3 AN: 1456698 Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1 AN XY: 724156

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000117

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.01e-7

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Rhabdoid tumor predisposition syndrome 2 Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 27, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 03, 2022	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. 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. ClinVar contains an entry for this variant (Variation ID: 1050905). This variant has not been reported in the literature in individuals affected with SMARCA4-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces isoleucine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 462 of the SMARCA4 protein (p.Ile462Met). -

Hereditary cancer-predisposing syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 10, 2024

The p.I462M variant (also known as c.1386C>G), located in coding exon 7 of the SMARCA4 gene, results from a C to G substitution at nucleotide position 1386. The isoleucine at codon 462 is replaced by methionine, 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. Based on the supporting evidence, the association of this alteration with Coffin-Siris syndrome is unknown; however, the association of this alteration with rhabdoid tumor predisposition syndrome is unlikely. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.34
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.38
CADD	Benign	0.42
DANN	Benign	0.80
DEOGEN2	Benign	0.22	T;.;T;.;.;.;.;.;.;.;T;.;.;.;.;.;T;T
Eigen	Benign	-2.2
Eigen_PC	Benign	-2.1
FATHMM_MKL	Benign	0.086	N
LIST_S2	Uncertain	0.94	.;D;.;.;.;.;D;.;.;.;D;.;D;D;D;D;D;D
M_CAP	Benign	0.080	D
MetaRNN	Benign	0.041	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.89	T
MutationAssessor	Benign	-1.8	N;.;.;.;N;N;.;N;N;N;N;N;N;N;N;N;.;.
PrimateAI	Pathogenic	0.85	D
PROVEAN	Benign	-0.16	N;.;.;.;.;.;.;.;.;.;N;.;N;.;N;.;N;N
REVEL	Uncertain	0.32
Sift	Benign	0.50	T;.;.;.;.;.;.;.;.;.;T;.;T;.;T;.;T;T
Sift4G	Benign	0.34	T;.;.;.;.;.;.;.;.;.;T;.;T;T;T;T;T;T
Polyphen		0.25	B;.;B;.;.;.;.;.;.;.;B;.;.;.;.;.;.;B
Vest4		0.60
MutPred		0.46		Loss of methylation at K461 (P = 0.0318);Loss of methylation at K461 (P = 0.0318);Loss of methylation at K461 (P = 0.0318);Loss of methylation at K461 (P = 0.0318);Loss of methylation at K461 (P = 0.0318);Loss of methylation at K461 (P = 0.0318);Loss of methylation at K461 (P = 0.0318);Loss of methylation at K461 (P = 0.0318);Loss of methylation at K461 (P = 0.0318);Loss of methylation at K461 (P = 0.0318);Loss of methylation at K461 (P = 0.0318);Loss of methylation at K461 (P = 0.0318);Loss of methylation at K461 (P = 0.0318);Loss of methylation at K461 (P = 0.0318);Loss of methylation at K461 (P = 0.0318);Loss of methylation at K461 (P = 0.0318);Loss of methylation at K461 (P = 0.0318);Loss of methylation at K461 (P = 0.0318);
MVP		0.74
MPC		2.5
ClinPred		0.17	T
GERP RS		-9.7
Varity_R		0.093
gMVP		0.96

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: rs1265247876; hg19: chr19-11101966;