19-11021968-G-C

Variant names:

• chr19-11021968-G-C
• rs797044856
• NM_001387283.1:c.2859+1G>C

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_Moderate PM2 PP5_Moderate

The NM_003072.5(SMARCA4):​c.2859+1G>C variant causes a splice donor, intron 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. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: SMARCA4 NM_003072.5 splice_donor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 9.89

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 Likely_pathogenic. Variant got 6 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.049150486 fraction of the gene. Cryptic splice site detected, with MaxEntScore 9.1, offset of 38, new splice context is: cagGTgcgg. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 19-11021968-G-C is Pathogenic according to our data. Variant chr19-11021968-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 208651.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.2859+1G>C		splice_donor_variant, intron_variant	Intron 19 of 35	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.2859+1G>C		splice_donor_variant, intron_variant	Intron 19 of 34	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.2859+1G>C		splice_donor_variant, intron_variant	Intron 19 of 35		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.2859+1G>C		splice_donor_variant, intron_variant	Intron 19 of 34	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.2859+1G>C		splice_donor_variant, intron_variant	Intron 19 of 34			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.2859+1G>C		splice_donor_variant, intron_variant	Intron 20 of 34	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.2859+1G>C		splice_donor_variant, intron_variant	Intron 19 of 33			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.2859+1G>C		splice_donor_variant, intron_variant	Intron 19 of 33			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.2859+1G>C		splice_donor_variant, intron_variant	Intron 20 of 34	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.2271+1G>C		splice_donor_variant, intron_variant	Intron 16 of 31			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.1503+1G>C		splice_donor_variant, intron_variant	Intron 12 of 27			ENSP00000495599.1
SMARCA4	ENST00000644065.1	c.1584+1G>C		splice_donor_variant, intron_variant	Intron 12 of 26			ENSP00000493615.1
SMARCA4	ENST00000642350.1	c.1344+1G>C		splice_donor_variant, intron_variant	Intron 11 of 26			ENSP00000495355.1
SMARCA4	ENST00000643857.1	c.1212+1G>C		splice_donor_variant, intron_variant	Intron 10 of 24			ENSP00000494159.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:1

Feb 28, 2019

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.2859+1G>C intronic variant results from a G to C substitution one nucleotide after coding exon 18 of the SMARCA4 gene. This alteration has been identified in two individuals diagnosed with small cell carcinoma of the ovary, hypercalcemic type from one family, and this alteration was found to cause skipping of exon 19 (Witkowski L et al. Fam. Cancer, 2017 07;16:395-399). This nucleotide position is highly conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to abolish the native splice donor site; however, direct evidence is unavailable. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as likely pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Uncertain	0.12
CADD	Pathogenic	36
DANN	Uncertain	0.99
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.84
FATHMM_MKL	Pathogenic	1.0	D
GERP RS		4.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.96		Position offset: 37
DS_DL_spliceai		0.99		Position offset: -1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs797044856; hg19: chr19-11132644;