19-11013021-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_003072.5(SMARCA4):c.2347C>T(p.Leu783Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000489 in 1,614,002 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. L783L) has been classified as Likely benign.
Frequency
Consequence
NM_003072.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMARCA4 | NM_001387283.1 | c.2347C>T | p.Leu783Leu | synonymous_variant | Exon 16 of 36 | ENST00000646693.2 | NP_001374212.1 | |
SMARCA4 | NM_003072.5 | c.2347C>T | p.Leu783Leu | synonymous_variant | Exon 16 of 35 | ENST00000344626.10 | NP_003063.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMARCA4 | ENST00000646693.2 | c.2347C>T | p.Leu783Leu | synonymous_variant | Exon 16 of 36 | NM_001387283.1 | ENSP00000495368.1 | |||
SMARCA4 | ENST00000344626.10 | c.2347C>T | p.Leu783Leu | synonymous_variant | Exon 16 of 35 | 1 | NM_003072.5 | ENSP00000343896.4 | ||
SMARCA4 | ENST00000643549.1 | c.2347C>T | p.Leu783Leu | synonymous_variant | Exon 16 of 35 | ENSP00000493975.1 | ||||
SMARCA4 | ENST00000541122.6 | c.2347C>T | p.Leu783Leu | synonymous_variant | Exon 17 of 35 | 5 | ENSP00000445036.2 | |||
SMARCA4 | ENST00000643296.1 | c.2347C>T | p.Leu783Leu | synonymous_variant | Exon 16 of 34 | ENSP00000496635.1 | ||||
SMARCA4 | ENST00000644737.1 | c.2347C>T | p.Leu783Leu | synonymous_variant | Exon 16 of 34 | ENSP00000495548.1 | ||||
SMARCA4 | ENST00000589677.5 | c.2347C>T | p.Leu783Leu | synonymous_variant | Exon 17 of 35 | 5 | ENSP00000464778.1 | |||
SMARCA4 | ENST00000643995.1 | c.1759C>T | p.Leu587Leu | synonymous_variant | Exon 13 of 32 | ENSP00000496004.1 | ||||
SMARCA4 | ENST00000644963.1 | c.991C>T | p.Leu331Leu | synonymous_variant | Exon 9 of 28 | ENSP00000495599.1 | ||||
SMARCA4 | ENST00000644065.1 | c.1072C>T | p.Leu358Leu | synonymous_variant | Exon 9 of 27 | ENSP00000493615.1 | ||||
SMARCA4 | ENST00000642350.1 | c.832C>T | p.Leu278Leu | synonymous_variant | Exon 8 of 27 | ENSP00000495355.1 | ||||
SMARCA4 | ENST00000643857.1 | c.700C>T | p.Leu234Leu | synonymous_variant | Exon 7 of 25 | ENSP00000494159.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000143 AC: 36AN: 251476Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135922
GnomAD4 exome AF: 0.0000527 AC: 77AN: 1461816Hom.: 0 Cov.: 31 AF XY: 0.0000866 AC XY: 63AN XY: 727222
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Benign:2
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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. -
Intellectual disability, autosomal dominant 16 Benign:1
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Rhabdoid tumor predisposition syndrome 2 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at