19-11061786-C-T

Variant names:

• chr19-11061786-C-T
• rs1555797441
• NM_001387283.1:c.5010C>T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2 BP4_Moderate BP6_Very_Strong BP7

The NM_003072.5(SMARCA4):​c.4914C>T​(p.Asp1638Asp) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,206 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency: Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
• Consequence: SMARCA4 NM_003072.5 splice_region, synonymous
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.997

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 Benign. Variant got -9 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BP6: Variant 19-11061786-C-T is Benign according to our data. Variant chr19-11061786-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 470434.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=0.997 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.5010C>T	p.Asp1670Asp	splice_region_variant, synonymous_variant	Exon 36 of 36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.4914C>T	p.Asp1638Asp	splice_region_variant, synonymous_variant	Exon 35 of 35	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.5010C>T	p.Asp1670Asp	splice_region_variant, synonymous_variant	Exon 36 of 36		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.4914C>T	p.Asp1638Asp	splice_region_variant, synonymous_variant	Exon 35 of 35	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.4920C>T	p.Asp1640Asp	splice_region_variant, synonymous_variant	Exon 35 of 35			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.4824C>T	p.Asp1608Asp	splice_region_variant, synonymous_variant	Exon 35 of 35	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.4824C>T	p.Asp1608Asp	splice_region_variant, synonymous_variant	Exon 34 of 34			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.4824C>T	p.Asp1608Asp	splice_region_variant, synonymous_variant	Exon 34 of 34			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.4821C>T	p.Asp1607Asp	splice_region_variant, synonymous_variant	Exon 35 of 35	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.4335C>T	p.Asp1445Asp	splice_region_variant, synonymous_variant	Exon 32 of 32			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.3564C>T	p.Asp1188Asp	splice_region_variant, synonymous_variant	Exon 28 of 28			ENSP00000495599.1
SMARCA4	ENST00000644065.1	c.3546C>T	p.Asp1182Asp	splice_region_variant, synonymous_variant	Exon 27 of 27			ENSP00000493615.1
SMARCA4	ENST00000642350.1	c.3408C>T	p.Asp1136Asp	splice_region_variant, synonymous_variant	Exon 27 of 27			ENSP00000495355.1
SMARCA4	ENST00000643857.1	c.3174C>T	p.Asp1058Asp	splice_region_variant, synonymous_variant	Exon 25 of 25			ENSP00000494159.1
SMARCA4	ENST00000538456.4	c.978C>T	p.Asp326Asp	splice_region_variant, synonymous_variant	Exon 8 of 8	3		ENSP00000495197.1

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152206 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 30

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152206 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 74362

Gnomad4 AFR AF: 0.0000241

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Rhabdoid tumor predisposition syndrome 2 Benign:1

Sep 10, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome Benign:1

Oct 23, 2015

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	11
DANN	Benign	0.85
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs1555797441; hg19: chr19-11172462;