19-10984297-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP2

The NM_001387283.1(SMARCA4):​c.146C>A​(p.Pro49Gln) variant causes a missense change involving the alteration of a 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)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

SMARCA4
NM_001387283.1 missense

Scores

4
11
4

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.86
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 3 ACMG points.

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.146C>A p.Pro49Gln missense_variant 2/36 ENST00000646693.2 NP_001374212.1
SMARCA4NM_003072.5 linkuse as main transcriptc.146C>A p.Pro49Gln missense_variant 2/35 ENST00000344626.10 NP_003063.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SMARCA4ENST00000646693.2 linkuse as main transcriptc.146C>A p.Pro49Gln missense_variant 2/36 NM_001387283.1 ENSP00000495368
SMARCA4ENST00000344626.10 linkuse as main transcriptc.146C>A p.Pro49Gln missense_variant 2/351 NM_003072.5 ENSP00000343896 P4P51532-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1455820
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
723860
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:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.31
BayesDel_addAF
Uncertain
0.16
D
BayesDel_noAF
Uncertain
-0.010
CADD
Uncertain
24
DANN
Uncertain
0.98
DEOGEN2
Uncertain
0.67
D;.;T;.;.;.;.;.;.;.;D;.;.;.;.;.;.;T;T
Eigen
Uncertain
0.66
Eigen_PC
Uncertain
0.62
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Pathogenic
0.98
.;D;.;.;.;.;D;.;.;.;D;D;.;D;D;D;D;D;D
M_CAP
Pathogenic
0.37
D
MetaRNN
Uncertain
0.60
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
0.54
D
MutationAssessor
Benign
1.1
L;.;.;.;L;L;.;L;L;L;L;.;L;L;L;L;L;.;.
MutationTaster
Benign
1.0
D;D;D;D;D;D;D;D;D
PrimateAI
Uncertain
0.68
T
PROVEAN
Uncertain
-2.8
D;.;.;.;.;.;.;.;.;.;D;.;.;D;.;D;.;D;D
REVEL
Uncertain
0.46
Sift
Pathogenic
0.0
D;.;.;.;.;.;.;.;.;.;D;.;.;D;.;D;.;D;D
Sift4G
Benign
0.13
T;.;.;.;.;.;.;.;.;.;T;.;.;T;T;T;T;T;T
Polyphen
1.0
D;.;D;.;.;.;.;.;.;.;D;.;.;.;.;.;.;.;D
Vest4
0.61
MutPred
0.19
Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);Loss of glycosylation at P49 (P = 0.0094);
MVP
0.77
MPC
0.24
ClinPred
0.96
D
GERP RS
5.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.42
gMVP
0.095

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: chr19-11094973; API