19-11058901-G-T

Variant names:

• chr19-11058901-G-T
• NM_001387283.1:c.4731+12G>T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_003072.5(SMARCA4):​c.4635+12G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000962 in 1,455,764 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000096 (0 hom.)
• Consequence: SMARCA4 NM_003072.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.18

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 19-11058901-G-T is Benign according to our data. Variant chr19-11058901-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1558259.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAdExome4 at 14 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.4731+12G>T		intron_variant	Intron 33 of 35	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.4635+12G>T		intron_variant	Intron 32 of 34	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.4731+12G>T		intron_variant	Intron 33 of 35		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.4635+12G>T		intron_variant	Intron 32 of 34	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.4641+12G>T		intron_variant	Intron 32 of 34			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.4545+12G>T		intron_variant	Intron 32 of 34	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.4545+12G>T		intron_variant	Intron 31 of 33			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.4545+12G>T		intron_variant	Intron 31 of 33			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.4542+12G>T		intron_variant	Intron 32 of 34	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.4056+12G>T		intron_variant	Intron 29 of 31			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.3285+12G>T		intron_variant	Intron 25 of 27			ENSP00000495599.1
SMARCA4	ENST00000644065.1	c.3267+12G>T		intron_variant	Intron 24 of 26			ENSP00000493615.1
SMARCA4	ENST00000642350.1	c.3129+12G>T		intron_variant	Intron 24 of 26			ENSP00000495355.1
SMARCA4	ENST00000643857.1	c.2895+538G>T		intron_variant	Intron 22 of 24			ENSP00000494159.1
SMARCA4	ENST00000538456.4	c.699+538G>T		intron_variant	Intron 5 of 7	3		ENSP00000495197.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000962 AC: 14 AN: 1455764 Hom.: 0 Cov.: 29 AF XY: 0.00000966 AC XY: 7 AN XY: 724582

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: 0.0000126

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Rhabdoid tumor predisposition syndrome 2 Benign:1

Jul 03, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.84
DANN	Benign	0.63

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-11169577;