rs369724341

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP2

The NM_003072.5(SMARCA4):​c.2562C>A​(p.Asn854Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

SMARCA4
NM_003072.5 missense

Scores

5
8
6

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.82
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 5 ACMG points.

PM1
In a region_of_interest Sufficient for interaction with DLX1 (size 79) in uniprot entity SMCA4_HUMAN there are 7 pathogenic changes around while only 0 benign (100%) in NM_003072.5
PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), SMARCA4. . Gene score misZ 6.8459 (greater than the threshold 3.09). Trascript score misZ 8.7957 (greater than threshold 3.09). GenCC has associacion of gene with uterine corpus sarcoma, Coffin-Siris syndrome 1, intellectual disability, autosomal dominant 16, rhabdoid tumor predisposition syndrome 2, familial rhabdoid tumor, hereditary nonpolyposis colon cancer, Coffin-Siris syndrome.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SMARCA4NM_001387283.1 linkuse as main transcriptc.2562C>A p.Asn854Lys missense_variant 18/36 ENST00000646693.2 NP_001374212.1
SMARCA4NM_003072.5 linkuse as main transcriptc.2562C>A p.Asn854Lys missense_variant 18/35 ENST00000344626.10 NP_003063.2 P51532-1A7E2E1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SMARCA4ENST00000646693.2 linkuse as main transcriptc.2562C>A p.Asn854Lys missense_variant 18/36 NM_001387283.1 ENSP00000495368.1 Q9HBD4
SMARCA4ENST00000344626.10 linkuse as main transcriptc.2562C>A p.Asn854Lys missense_variant 18/351 NM_003072.5 ENSP00000343896.4 P51532-1
SMARCA4ENST00000643549.1 linkuse as main transcriptc.2562C>A p.Asn854Lys missense_variant 18/35 ENSP00000493975.1 A0A2R8Y4P4
SMARCA4ENST00000541122.6 linkuse as main transcriptc.2562C>A p.Asn854Lys missense_variant 19/355 ENSP00000445036.2 P51532-4
SMARCA4ENST00000643296.1 linkuse as main transcriptc.2562C>A p.Asn854Lys missense_variant 18/34 ENSP00000496635.1 P51532-4
SMARCA4ENST00000644737.1 linkuse as main transcriptc.2562C>A p.Asn854Lys missense_variant 18/34 ENSP00000495548.1 P51532-4
SMARCA4ENST00000589677.5 linkuse as main transcriptc.2562C>A p.Asn854Lys missense_variant 19/355 ENSP00000464778.1 P51532-3
SMARCA4ENST00000643995.1 linkuse as main transcriptc.1974C>A p.Asn658Lys missense_variant 15/32 ENSP00000496004.1 A0A2R8YGG3
SMARCA4ENST00000644963.1 linkuse as main transcriptc.1206C>A p.Asn402Lys missense_variant 11/28 ENSP00000495599.1 A0A2R8YG32
SMARCA4ENST00000644065.1 linkuse as main transcriptc.1287C>A p.Asn429Lys missense_variant 11/27 ENSP00000493615.1 A0A2R8Y440
SMARCA4ENST00000642350.1 linkuse as main transcriptc.1047C>A p.Asn349Lys missense_variant 10/27 ENSP00000495355.1 A0A2R8Y6N0
SMARCA4ENST00000643857.1 linkuse as main transcriptc.915C>A p.Asn305Lys missense_variant 9/25 ENSP00000494159.1 A0A2R8Y526

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
1.0
BayesDel_addAF
Uncertain
0.070
D
BayesDel_noAF
Benign
-0.14
CADD
Benign
12
DANN
Uncertain
0.99
DEOGEN2
Pathogenic
0.94
D;.;D;.;.;.;.;.;.;.;D;.;.;.;.;.;T;D;.;.;.;.
Eigen
Benign
-0.80
Eigen_PC
Benign
-1.1
FATHMM_MKL
Benign
0.21
N
LIST_S2
Uncertain
0.97
.;D;.;.;.;.;D;.;.;.;D;.;D;D;D;D;D;D;D;D;D;D
M_CAP
Pathogenic
0.86
D
MetaRNN
Uncertain
0.67
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
0.62
D
MutationAssessor
Benign
1.6
L;.;.;.;L;L;.;L;L;L;L;L;L;L;L;L;.;.;.;.;.;.
PrimateAI
Pathogenic
0.87
D
PROVEAN
Pathogenic
-5.4
D;.;.;.;.;.;.;.;.;.;D;.;D;.;D;.;.;D;.;.;.;.
REVEL
Uncertain
0.53
Sift
Uncertain
0.0030
D;.;.;.;.;.;.;.;.;.;D;.;D;.;D;.;.;D;.;.;.;.
Sift4G
Uncertain
0.0090
D;.;.;.;.;.;.;.;.;.;D;.;D;D;D;D;D;D;.;.;.;.
Polyphen
1.0
D;.;D;.;.;.;.;.;.;.;D;.;.;.;.;.;.;D;.;.;.;.
Vest4
0.86
MutPred
0.65
Gain of methylation at N854 (P = 0.0037);Gain of methylation at N854 (P = 0.0037);Gain of methylation at N854 (P = 0.0037);Gain of methylation at N854 (P = 0.0037);Gain of methylation at N854 (P = 0.0037);Gain of methylation at N854 (P = 0.0037);Gain of methylation at N854 (P = 0.0037);Gain of methylation at N854 (P = 0.0037);Gain of methylation at N854 (P = 0.0037);Gain of methylation at N854 (P = 0.0037);Gain of methylation at N854 (P = 0.0037);Gain of methylation at N854 (P = 0.0037);Gain of methylation at N854 (P = 0.0037);Gain of methylation at N854 (P = 0.0037);Gain of methylation at N854 (P = 0.0037);Gain of methylation at N854 (P = 0.0037);.;Gain of methylation at N854 (P = 0.0037);.;.;.;.;
MVP
0.87
MPC
3.5
ClinPred
0.98
D
GERP RS
-7.6
RBP_binding_hub_radar
0.92
RBP_regulation_power_radar
2.7
Varity_R
0.96
gMVP
0.97

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: chr19-11130323; API