19-11060193-G-T

Variant names:

• chr19-11060193-G-T
• rs878854235
• NM_001387283.1:c.5007+6G>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003072.5(SMARCA4):​c.4911+6G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SMARCA4 NM_003072.5 splice_region, intron
• Scores: Splicing: ADA: 0.0001797
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.273

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_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.5007+6G>T		splice_region_variant, intron_variant	Intron 35 of 35	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.4911+6G>T		splice_region_variant, intron_variant	Intron 34 of 34	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.5007+6G>T		splice_region_variant, intron_variant	Intron 35 of 35		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.4911+6G>T		splice_region_variant, intron_variant	Intron 34 of 34	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.4917+6G>T		splice_region_variant, intron_variant	Intron 34 of 34			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.4821+6G>T		splice_region_variant, intron_variant	Intron 34 of 34	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.4821+6G>T		splice_region_variant, intron_variant	Intron 33 of 33			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.4821+6G>T		splice_region_variant, intron_variant	Intron 33 of 33			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.4818+6G>T		splice_region_variant, intron_variant	Intron 34 of 34	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.4332+6G>T		splice_region_variant, intron_variant	Intron 31 of 31			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.3561+6G>T		splice_region_variant, intron_variant	Intron 27 of 27			ENSP00000495599.1
SMARCA4	ENST00000644065.1	c.3543+6G>T		splice_region_variant, intron_variant	Intron 26 of 26			ENSP00000493615.1
SMARCA4	ENST00000642350.1	c.3405+6G>T		splice_region_variant, intron_variant	Intron 26 of 26			ENSP00000495355.1
SMARCA4	ENST00000643857.1	c.3171+6G>T		splice_region_variant, intron_variant	Intron 24 of 24			ENSP00000494159.1
SMARCA4	ENST00000538456.4	c.975+6G>T		splice_region_variant, intron_variant	Intron 7 of 7	3		ENSP00000495197.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1398346 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 689692

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Rhabdoid tumor predisposition syndrome 2 Uncertain:1

Sep 01, 2021

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change falls in intron 35 of the SMARCA4 gene. It does not directly change the encoded amino acid sequence of the SMARCA4 protein. It affects a nucleotide within the consensus splice site of the intron. This variant is not present in population databases (ExAC 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: 238501). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.0
DANN	Benign	0.63
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00018
dbscSNV1_RF	Benign	0.0
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: rs878854235; hg19: chr19-11170869;