rs1300802922
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_003072.5(SMARCA4):c.2682G>A(p.Thr894Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,461,370 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 (★★).
Frequency
Consequence
NM_003072.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMARCA4 | NM_001387283.1 | c.2682G>A | p.Thr894Thr | synonymous_variant | Exon 19 of 36 | ENST00000646693.2 | NP_001374212.1 | |
SMARCA4 | NM_003072.5 | c.2682G>A | p.Thr894Thr | synonymous_variant | Exon 19 of 35 | ENST00000344626.10 | NP_003063.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMARCA4 | ENST00000646693.2 | c.2682G>A | p.Thr894Thr | synonymous_variant | Exon 19 of 36 | NM_001387283.1 | ENSP00000495368.1 | |||
SMARCA4 | ENST00000344626.10 | c.2682G>A | p.Thr894Thr | synonymous_variant | Exon 19 of 35 | 1 | NM_003072.5 | ENSP00000343896.4 | ||
SMARCA4 | ENST00000643549.1 | c.2682G>A | p.Thr894Thr | synonymous_variant | Exon 19 of 35 | ENSP00000493975.1 | ||||
SMARCA4 | ENST00000541122.6 | c.2682G>A | p.Thr894Thr | synonymous_variant | Exon 20 of 35 | 5 | ENSP00000445036.2 | |||
SMARCA4 | ENST00000643296.1 | c.2682G>A | p.Thr894Thr | synonymous_variant | Exon 19 of 34 | ENSP00000496635.1 | ||||
SMARCA4 | ENST00000644737.1 | c.2682G>A | p.Thr894Thr | synonymous_variant | Exon 19 of 34 | ENSP00000495548.1 | ||||
SMARCA4 | ENST00000589677.5 | c.2682G>A | p.Thr894Thr | synonymous_variant | Exon 20 of 35 | 5 | ENSP00000464778.1 | |||
SMARCA4 | ENST00000643995.1 | c.2094G>A | p.Thr698Thr | synonymous_variant | Exon 16 of 32 | ENSP00000496004.1 | ||||
SMARCA4 | ENST00000644963.1 | c.1326G>A | p.Thr442Thr | synonymous_variant | Exon 12 of 28 | ENSP00000495599.1 | ||||
SMARCA4 | ENST00000644065.1 | c.1407G>A | p.Thr469Thr | synonymous_variant | Exon 12 of 27 | ENSP00000493615.1 | ||||
SMARCA4 | ENST00000642350.1 | c.1167G>A | p.Thr389Thr | synonymous_variant | Exon 11 of 27 | ENSP00000495355.1 | ||||
SMARCA4 | ENST00000643857.1 | c.1035G>A | p.Thr345Thr | synonymous_variant | Exon 10 of 25 | ENSP00000494159.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250568Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135652
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461370Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727008
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Benign:2
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. -
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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