chr19-11041336-C-T

Variant names:

• chr19-11041336-C-T
• rs577059244
• NM_001387283.1:c.4296C>T

Variant summary

Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_Moderate BP6_Very_Strong BP7 BS1

The NM_001387283.1(SMARCA4):​c.4296C>T​(p.Ile1432Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,611,750 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 (★★). Synonymous variant affecting the same amino acid position (i.e. I1432I) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000020 (0 hom.)
• Consequence: SMARCA4 NM_001387283.1 synonymous
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.48
• Publications: 2 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: Benign. The variant received -15 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BP6: Variant 19-11041336-C-T is Benign according to our data. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11041336-C-T is described in CliVar as Likely_benign. Clinvar id is 470392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-1.48 with no splicing effect.
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.0000197 (3/152118) while in subpopulation EAS AF = 0.000386 (2/5186). AF 95% confidence interval is 0.0000683. There are 0 homozygotes in GnomAd4. There are 2 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.4296C>T	p.Ile1432Ile	synonymous_variant	Exon 31 of 36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.4200C>T	p.Ile1400Ile	synonymous_variant	Exon 30 of 35	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.4296C>T	p.Ile1432Ile	synonymous_variant	Exon 31 of 36		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.4200C>T	p.Ile1400Ile	synonymous_variant	Exon 30 of 35	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.4206C>T	p.Ile1402Ile	synonymous_variant	Exon 30 of 35			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.4110C>T	p.Ile1370Ile	synonymous_variant	Exon 30 of 35	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.4110C>T	p.Ile1370Ile	synonymous_variant	Exon 29 of 34			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.4110C>T	p.Ile1370Ile	synonymous_variant	Exon 29 of 34			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.4110C>T	p.Ile1370Ile	synonymous_variant	Exon 30 of 35	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.3621C>T	p.Ile1207Ile	synonymous_variant	Exon 27 of 32			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.2853C>T	p.Ile951Ile	synonymous_variant	Exon 23 of 28			ENSP00000495599.1
SMARCA4	ENST00000644065.1	c.2835C>T	p.Ile945Ile	synonymous_variant	Exon 22 of 27			ENSP00000493615.1
SMARCA4	ENST00000642350.1	c.2694C>T	p.Ile898Ile	synonymous_variant	Exon 22 of 27			ENSP00000495355.1
SMARCA4	ENST00000643857.1	c.2562C>T	p.Ile854Ile	synonymous_variant	Exon 21 of 25			ENSP00000494159.1
SMARCA4	ENST00000538456.4	c.366C>T	p.Ile122Ile	synonymous_variant	Exon 4 of 8	3		ENSP00000495197.1

Frequencies

GnomAD3 genomes AF: 0.0000197 AC: 3 AN: 152118 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000386

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

GnomAD2 exomes AF: 0.0000444 AC: 11 AN: 247844 AF XY: 0.0000447

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000602

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000199 AC: 29 AN: 1459632 Hom.: 0 Cov.: 32 AF XY: 0.0000207 AC XY: 15 AN XY: 726160

African (AFR) AF: 0.00 AC: 0 AN: 33478

American (AMR) AF: 0.00 AC: 0 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26132

East Asian (EAS) AF: 0.000655 AC: 26 AN: 39694

South Asian (SAS) AF: 0.00 AC: 0 AN: 86248

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51274

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5754

European-Non Finnish (NFE) AF: 8.99e-7 AC: 1 AN: 1111944

Other (OTH) AF: 0.0000331 AC: 2 AN: 60384

GnomAD4 genome AF: 0.0000197 AC: 3 AN: 152118 Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2 AN XY: 74308

African (AFR) AF: 0.00 AC: 0 AN: 41412

American (AMR) AF: 0.0000655 AC: 1 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5186

South Asian (SAS) AF: 0.00 AC: 0 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10600

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68038

Other (OTH) AF: 0.00 AC: 0 AN: 2088

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000151

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

Aug 21, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome Benign:1

Aug 20, 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	-0.24
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		-1.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=98/2	polymorphism

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

Other links and lift over

dbSNP: rs577059244; hg19: chr19-11152012; COSMIC: COSV60793470; COSMIC: COSV60793470;