rs910572313

Variant names:

• chr19-11034905-G-A
• rs910572313
• NM_001387283.1:c.3952-9G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-11034905-G-A
• chr19-11034905-G-C
• chr19-11034905-G-T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP6

The NM_001387283.1(SMARCA4):​c.3952-9G>A variant causes a 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. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SMARCA4 NM_001387283.1 intron
• Scores: Splicing: ADA: 0.0003276
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:1
• Conservation: PhyloP100: -0.703
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• Coffin-Siris syndrome

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet, Illumina
• intellectual disability, autosomal dominant 16

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
• rhabdoid tumor predisposition syndrome 2

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, ClinGen, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), G2P
• uterine corpus sarcoma

  Inheritance: AR Classification: MODERATE Submitted by: Genomics England PanelApp
• familial rhabdoid tumor

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary nonpolyposis colon cancer

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 19-11034905-G-A is Benign according to our data. Variant chr19-11034905-G-A is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 772964.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.3952-9G>A		intron_variant	Intron 28 of 35	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.3952-9G>A		intron_variant	Intron 28 of 34	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.3952-9G>A		intron_variant	Intron 28 of 35		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.3952-9G>A		intron_variant	Intron 28 of 34	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.3853-9G>A		intron_variant	Intron 27 of 34			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.3853-9G>A		intron_variant	Intron 28 of 34	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.3853-9G>A		intron_variant	Intron 27 of 33			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.3853-9G>A		intron_variant	Intron 27 of 33			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.3853-9G>A		intron_variant	Intron 28 of 34	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.3364-9G>A		intron_variant	Intron 25 of 31			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.2596-9G>A		intron_variant	Intron 21 of 27			ENSP00000495599.1
SMARCA4	ENST00000644065.1	c.2578-9G>A		intron_variant	Intron 20 of 26			ENSP00000493615.1
SMARCA4	ENST00000642350.1	c.2437-9G>A		intron_variant	Intron 20 of 26			ENSP00000495355.1
SMARCA4	ENST00000643857.1	c.2305-9G>A		intron_variant	Intron 19 of 24			ENSP00000494159.1
SMARCA4	ENST00000538456.4	c.109-9G>A		intron_variant	Intron 2 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: 1400060 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 691494

African (AFR) AF: 0.00 AC: 0 AN: 31928

American (AMR) AF: 0.00 AC: 0 AN: 36282

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25202

East Asian (EAS) AF: 0.00 AC: 0 AN: 36436

South Asian (SAS) AF: 0.00 AC: 0 AN: 79650

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47810

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4240

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1080490

Other (OTH) AF: 0.00 AC: 0 AN: 58022

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hereditary cancer-predisposing syndrome Uncertain:1

Dec 22, 2021

Sema4, Sema4

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: curation

- -

Rhabdoid tumor predisposition syndrome 2 Benign:1

Jan 17, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.28
DANN	Benign	0.47
PhyloP100		-0.70
PromoterAI		0.0044	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00033
dbscSNV1_RF	Benign	0.012
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

Other links and lift over

dbSNP: rs910572313; hg19: chr19-11145581;