rs1555780015

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_003072.5(SMARCA4):​c.3021C>A​(p.Leu1007Leu) variant causes a synonymous 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. 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 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.501
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 Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SMARCA4NM_001387283.1 linkc.3021C>A p.Leu1007Leu synonymous_variant Exon 21 of 36 ENST00000646693.2 NP_001374212.1
SMARCA4NM_003072.5 linkc.3021C>A p.Leu1007Leu synonymous_variant Exon 21 of 35 ENST00000344626.10 NP_003063.2 P51532-1A7E2E1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SMARCA4ENST00000646693.2 linkc.3021C>A p.Leu1007Leu synonymous_variant Exon 21 of 36 NM_001387283.1 ENSP00000495368.1 Q9HBD4
SMARCA4ENST00000344626.10 linkc.3021C>A p.Leu1007Leu synonymous_variant Exon 21 of 35 1 NM_003072.5 ENSP00000343896.4 P51532-1
SMARCA4ENST00000643549.1 linkc.3021C>A p.Leu1007Leu synonymous_variant Exon 21 of 35 ENSP00000493975.1 A0A2R8Y4P4
SMARCA4ENST00000541122.6 linkc.3021C>A p.Leu1007Leu synonymous_variant Exon 22 of 35 5 ENSP00000445036.2 P51532-4
SMARCA4ENST00000643296.1 linkc.3021C>A p.Leu1007Leu synonymous_variant Exon 21 of 34 ENSP00000496635.1 P51532-4
SMARCA4ENST00000644737.1 linkc.3021C>A p.Leu1007Leu synonymous_variant Exon 21 of 34 ENSP00000495548.1 P51532-4
SMARCA4ENST00000589677.5 linkc.3021C>A p.Leu1007Leu synonymous_variant Exon 22 of 35 5 ENSP00000464778.1 P51532-3
SMARCA4ENST00000643995.1 linkc.2433C>A p.Leu811Leu synonymous_variant Exon 18 of 32 ENSP00000496004.1 A0A2R8YGG3
SMARCA4ENST00000644963.1 linkc.1665C>A p.Leu555Leu synonymous_variant Exon 14 of 28 ENSP00000495599.1 A0A2R8YG32
SMARCA4ENST00000644065.1 linkc.1746C>A p.Leu582Leu synonymous_variant Exon 14 of 27 ENSP00000493615.1 A0A2R8Y440
SMARCA4ENST00000642350.1 linkc.1506C>A p.Leu502Leu synonymous_variant Exon 13 of 27 ENSP00000495355.1 A0A2R8Y6N0
SMARCA4ENST00000643857.1 linkc.1374C>A p.Leu458Leu synonymous_variant Exon 12 of 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
BayesDel_noAF
Benign
-0.56
CADD
Benign
0.75
DANN
Benign
0.73
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.8

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: chr19-11135054; API